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sales@biotechnologyforums.com to feature here
sales@biotechnologyforums.com to feature here

by soumyag026 at 05-03-2017, 02:39 PM
0 comments
Dear all
I am a mechanical engineer presently servicing at a manufacturing industry. I have been planning for a tissue culture business farm from long back though I am not from the educational background required, but I love and have irresistible interest in the field from last 10 years.
In regard of business, i am planning for a partnership business in the field of both ground and underwater aquarium plants with starting of a smaller farm and later expansion to bigger farm with profit earned. I need some enlightenment in some specific areas that i am not aware of/ lacking of knowledge-
1. Domestic market feasibility at Bengal, demand and availability for ground plants, please mention the most demanding plants in the market that can be started with, please also mention the sales/marketing strategy that i need to adopt.
2. Financial help/subsidy available from government.
3. Manpower requirements and cost. Labour acts.
4. Approximate cost of setup of lab and machineries in a 6 kottah(4320 sq ft) land.
6. If i move further for export what should be the consideration that need to be taken in account from initial phase.
Kindly advise. Any help regarding the matter would be appreciated.
I am a mechanical engineer presently servicing at a manufacturing industry. I have been planning for a tissue culture business farm from long back though I am not from the educational background required, but I love and have irresistible interest in the field from last 10 years.
In regard of business, i am planning for a partnership business in the field of both ground and underwater aquarium plants with starting of a smaller farm and later expansion to bigger farm with profit earned. I need some enlightenment in some specific areas that i am not aware of/ lacking of knowledge-
1. Domestic market feasibility at Bengal, demand and availability for ground plants, please mention the most demanding plants in the market that can be started with, please also mention the sales/marketing strategy that i need to adopt.
2. Financial help/subsidy available from government.
3. Manpower requirements and cost. Labour acts.
4. Approximate cost of setup of lab and machineries in a 6 kottah(4320 sq ft) land.
6. If i move further for export what should be the consideration that need to be taken in account from initial phase.
Kindly advise. Any help regarding the matter would be appreciated.

by kriti khandelwal at 05-02-2017, 04:28 AM
2 comments
Sir/maam
I am a student of msc microbiology and immunology. I want to do industrial training for two months. Can you suggest me any companies where I can apply in North India.
I am a student of msc microbiology and immunology. I want to do industrial training for two months. Can you suggest me any companies where I can apply in North India.

by Pragya Anand at 05-02-2017, 12:25 AM
1 comments
What exact protocol is followed for SCP production for commercial purposes n how toxicity analysis of these protein are done to avoid side effects of these to human health?

by mansi at 05-01-2017, 04:21 AM
0 comments
Am in sy biotec very confused what to choose pls help me to know for msc which subject should I take

by bidyasagar at 04-30-2017, 07:04 PM
1 comments
Hi, everyone my name is bidyasagar pursuying my btech course,biotechnology last sem...i need some guideliness regarding the upcoming CEEB entrance exam..n which study materials(reference books) should i prefer for the same xm mentioned!!

by Bioentrepreneur at 04-30-2017, 01:58 PM
0 comments
Hello, I'm a CFA and run a research company, White Diamond Research. I would like to start a biotech company. I already have the investors who want to invest in a biotech, but we haven't settled on an idea yet. If you have a good drug idea, but not the funding, please let me know. I have an idea I've been working on, but still not sure if it would would be successful. It's a new indication for an existing antipsychotic drug. If you are knowledgeable about anti-psychotic drugs, feel free to contact me to discuss it. Send me an email at agefvert@whitediamondresearch.com.
Best,
Adam Gefvert, CFA
Best,
Adam Gefvert, CFA

by B.nandha kumar at 04-30-2017, 03:37 AM
1 comments
I am new in this group,
I am nandha Kumar ... I am pursuing final semester from b.Sc.,biotechnology ...
Suggest me m.sc., best college ...
Help me...
I am nandha Kumar ... I am pursuing final semester from b.Sc.,biotechnology ...
Suggest me m.sc., best college ...
Help me...

by Dmytro at 04-29-2017, 08:47 PM
0 comments
Hi everyone!
I'm new here, and i hope it's okay to ask and discuss some questions like that![[Image: smile.gif]](http://www.biotechnologyforums.com/images/smilies/smile.gif)
The question is simple, what do you think of this mechanism (constructed by me of course)? Is it good (link below is for google drive, JPG file, totally safe)
https://drive.google.com/file/d/0B0j65CD...sp=sharing
If you have any similar questions about chemistry, we can discuss them here.
Thank you for your attention!
I'm new here, and i hope it's okay to ask and discuss some questions like that
![[Image: smile.gif]](http://www.biotechnologyforums.com/images/smilies/smile.gif)
The question is simple, what do you think of this mechanism (constructed by me of course)? Is it good (link below is for google drive, JPG file, totally safe)
https://drive.google.com/file/d/0B0j65CD...sp=sharing
If you have any similar questions about chemistry, we can discuss them here.
Thank you for your attention!

by VedKamlesh at 04-28-2017, 03:47 PM
0 comments
Hi Sunil
My son just gave Class 10th CBSE Exam and has opted for PCB, He is adamant / firm on taking up Biotechnology and go in Pure research
What would be the Path Like?
How he should prepare for next 2 years?
Does he Opt for BSC or still he can pursue B Tech
Thanks in advance for the Help
My son just gave Class 10th CBSE Exam and has opted for PCB, He is adamant / firm on taking up Biotechnology and go in Pure research

What would be the Path Like?
How he should prepare for next 2 years?
Does he Opt for BSC or still he can pursue B Tech
Thanks in advance for the Help


by Tomisin at 04-28-2017, 05:42 AM
0 comments
Hello I'm currently a 2nd year student of biotechnology b.Tech, and I want to know what it entails for me to do my masters in a medical inclined course and also the types of medical courses available.

by binu at 04-25-2017, 03:18 PM
0 comments
Question:
Intra Molecular Distance Matrix calculation (50 marks) : ATOM lines (155) of a pdb file are provided in input file (only C@ residues). Calculate intra molecular distance between each C@ residue. If distance >= 6, print 1 in distance matrix of output file, else print 0 in distance matrix.
Solution:
#!/usr/bin/perl -w
# Perl program to calculate intra molecular distance
use strict;
my ($file,$line,@array_x,@array_y,@array_z,$dist,$j,$i,$element);
my $k=0;
print "Enter the PDB filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or die "Cannot open file $file \n\n" ;
while ($line = <FILE>)
{
if ($line =~ /^ATOM/)
{
$array_x[$k] = (split (/\s+/, $line))[6];
$array_y[$k] = (split (/\s+/, $line))[7];
$array_z[$k] = (split (/\s+/, $line))[8];
$k++;
}
}
close FILE;
#print "K=$k \n";
#print "@array_x \n @array_y \n @array_z \n";
print "\n Intramolecular Distance Matrix is : \n\n";
print "ATOMi \t ATOMj \t Euclidean Distance \t Element \n";
for($i = 0; $i < $k ; $i++)
{
for($j = 0; $j < $k ; $j++)
{
#Euclidean Distance Calculation
$dist = sqrt(
($array_x[$i] - $array_x[$j])**2 +
($array_y[$i] - $array_y[$j])**2 +
($array_z[$i] - $array_z[$j])**2
);
if ($dist >= 6)
{
$element = 1;
print "$i \t $j \t $dist \t $element \n";
}
else
{
$element = 0;
print "$i \t $j \t $dist \t $element \n";
}
}
}
Intra Molecular Distance Matrix calculation (50 marks) : ATOM lines (155) of a pdb file are provided in input file (only C@ residues). Calculate intra molecular distance between each C@ residue. If distance >= 6, print 1 in distance matrix of output file, else print 0 in distance matrix.
Solution:
#!/usr/bin/perl -w
# Perl program to calculate intra molecular distance
use strict;
my ($file,$line,@array_x,@array_y,@array_z,$dist,$j,$i,$element);
my $k=0;
print "Enter the PDB filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or die "Cannot open file $file \n\n" ;
while ($line = <FILE>)
{
if ($line =~ /^ATOM/)
{
$array_x[$k] = (split (/\s+/, $line))[6];
$array_y[$k] = (split (/\s+/, $line))[7];
$array_z[$k] = (split (/\s+/, $line))[8];
$k++;
}
}
close FILE;
#print "K=$k \n";
#print "@array_x \n @array_y \n @array_z \n";
print "\n Intramolecular Distance Matrix is : \n\n";
print "ATOMi \t ATOMj \t Euclidean Distance \t Element \n";
for($i = 0; $i < $k ; $i++)
{
for($j = 0; $j < $k ; $j++)
{
#Euclidean Distance Calculation
$dist = sqrt(
($array_x[$i] - $array_x[$j])**2 +
($array_y[$i] - $array_y[$j])**2 +
($array_z[$i] - $array_z[$j])**2
);
if ($dist >= 6)
{
$element = 1;
print "$i \t $j \t $dist \t $element \n";
}
else
{
$element = 0;
print "$i \t $j \t $dist \t $element \n";
}
}
}

by binu at 04-25-2017, 03:13 PM
0 comments
Question :
i) An autocatalytic reaction is described by the expression
x/P = [exp(at) -1]/ [1 + b exp(at)], with a= ( A +P)k and b = P/A.
Write a program in C or JAVA or Perl or PYTHON to calculate x/P for three values of t (t =1,2 and 3)
using a & b as given in the input file autocat.dat.
Report if the saturation is reached by printing a string, “The saturation is reached. The values
are” and then print the value of ( x/P, a, b and t) for the saturation point.
Otherwise, print the message “ The Saturation is not reached” . All your output, including
these messages is to be saved in a file called autocat.out.
Solution :
#!/usr/bin/perl -w
# BINC 2015 sample question paper 3 solution
use strict;
my ($line,@arraya,@arrayb,$xp,$t,$j);
my $i=0;
open (FILE, "autocat.dat.txt") or
die "Cannot open file \n\n" ;
while ($line = <FILE>)
{
if ($line =~ /^a/ )
{ next; }
else
{
$arraya[$i] = (split (/\s+/, $line))[0];
$arrayb[$i] = (split (/\s+/, $line))[1];
$i++;
}
}
close FILE;
$j=$i;
print "The value of J=$j \n";
open (OUTPUT, ">autocat.out");
for ($t=1;$t<4;$t++)
{
for($i=0;$i<$j;$i++)
{
$xp = (exp($arraya[$i]*$t) -1) / (1 + ($arrayb[$i]*exp($arraya[$i]*$t)));
print "When T=$t the value of XP=$xp \n";
if ($xp==100)
{
print "The saturation is reached. The values are : \nXP=$xp \na=$arraya[$i] \nb=$arrayb[$i] \nt=$t\n\n";
print OUTPUT "The saturation is reached. The values are : \nXP=$xp \na=$arraya[$i] \nb=$arrayb[$i] \nt=$t\n\n";
}
else
{
print "The Saturation is not reached \n\n";
print OUTPUT "The Saturation is not reached \n\n";
}
}
}
close OUTPUT;
i) An autocatalytic reaction is described by the expression
x/P = [exp(at) -1]/ [1 + b exp(at)], with a= ( A +P)k and b = P/A.
Write a program in C or JAVA or Perl or PYTHON to calculate x/P for three values of t (t =1,2 and 3)
using a & b as given in the input file autocat.dat.
Report if the saturation is reached by printing a string, “The saturation is reached. The values
are” and then print the value of ( x/P, a, b and t) for the saturation point.
Otherwise, print the message “ The Saturation is not reached” . All your output, including
these messages is to be saved in a file called autocat.out.
Solution :
#!/usr/bin/perl -w
# BINC 2015 sample question paper 3 solution
use strict;
my ($line,@arraya,@arrayb,$xp,$t,$j);
my $i=0;
open (FILE, "autocat.dat.txt") or
die "Cannot open file \n\n" ;
while ($line = <FILE>)
{
if ($line =~ /^a/ )
{ next; }
else
{
$arraya[$i] = (split (/\s+/, $line))[0];
$arrayb[$i] = (split (/\s+/, $line))[1];
$i++;
}
}
close FILE;
$j=$i;
print "The value of J=$j \n";
open (OUTPUT, ">autocat.out");
for ($t=1;$t<4;$t++)
{
for($i=0;$i<$j;$i++)
{
$xp = (exp($arraya[$i]*$t) -1) / (1 + ($arrayb[$i]*exp($arraya[$i]*$t)));
print "When T=$t the value of XP=$xp \n";
if ($xp==100)
{
print "The saturation is reached. The values are : \nXP=$xp \na=$arraya[$i] \nb=$arrayb[$i] \nt=$t\n\n";
print OUTPUT "The saturation is reached. The values are : \nXP=$xp \na=$arraya[$i] \nb=$arrayb[$i] \nt=$t\n\n";
}
else
{
print "The Saturation is not reached \n\n";
print OUTPUT "The Saturation is not reached \n\n";
}
}
}
close OUTPUT;

by binu at 04-25-2017, 03:05 PM
0 comments
print "Enter elements in matrix A of size 3x3: \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$A[$row][$col] = <STDIN>;
}
}
print "Enter elements in matrix B of size 3x3: \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$B[$row][$col] = <STDIN>;
}
}
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$C[$row][$col] = $A[$row][$col] + $B[$row][$col] ;
}
}
print "Sum of the Matrices A+B is : \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $C[$row][$col]);
}
print "\n";
}
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$A[$row][$col] = <STDIN>;
}
}
print "Enter elements in matrix B of size 3x3: \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$B[$row][$col] = <STDIN>;
}
}
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$C[$row][$col] = $A[$row][$col] + $B[$row][$col] ;
}
}
print "Sum of the Matrices A+B is : \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $C[$row][$col]);
}
print "\n";
}

by binu at 04-25-2017, 03:04 PM
0 comments
print "Enter 3*3 Array Elements : ";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$matrix[$row][$col] = <STDIN>;
}
}
# Print the original matrix
print "Entered Matrix is : \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $matrix[$row][$col]);
}
print "\n";
}
#Transposing the matrix
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$matrix_transpose[$row][$col] = $matrix[$col][$row];
}
}
# Print the matrix in 3 integer spaces : "%3d"
print "Transpose of the Matrix is :\n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $matrix_transpose[$row][$col]);
}
print "\n";
}
# Check for Symmetric Matrix
$isSymmetric = 0;
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
if ($matrix[$row][$col] != $matrix[$col][$row])
{ $isSymmetric = 1; print $isSymmetric; }
}
}
if($isSymmetric==0)
{ print("Matrix is symmetric. \n"); }
else
{ print("Matrix is not symmetric. \n"); }
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$matrix[$row][$col] = <STDIN>;
}
}
# Print the original matrix
print "Entered Matrix is : \n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $matrix[$row][$col]);
}
print "\n";
}
#Transposing the matrix
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
$matrix_transpose[$row][$col] = $matrix[$col][$row];
}
}
# Print the matrix in 3 integer spaces : "%3d"
print "Transpose of the Matrix is :\n";
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
printf("%3d", $matrix_transpose[$row][$col]);
}
print "\n";
}
# Check for Symmetric Matrix
$isSymmetric = 0;
for($row=0; $row<3 ; $row++)
{
for($col=0; $col<3 ; $col++)
{
if ($matrix[$row][$col] != $matrix[$col][$row])
{ $isSymmetric = 1; print $isSymmetric; }
}
}
if($isSymmetric==0)
{ print("Matrix is symmetric. \n"); }
else
{ print("Matrix is not symmetric. \n"); }

by binu at 04-24-2017, 05:46 PM
0 comments
#!/usr/bin/perl -w
use strict;
my ($file,$line,$dna,$revcom,$i,$codon,@frames_array,$j,$orf);
my ($frame1,$frame2,$frame3,$frame4,$frame5,$frame6)='';
print "Enter the filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or
die "Cannot open file : $file \n\n";
while ($line = <FILE>)
{
if ($line =~ /^#/ )
{ next; }
elsif($line =~ /^>/ )
{ next; }
else
{ $dna .= $line; }
}
$dna =~ s/\s//g ;
close FILE;
print "Original Sequence is: $dna \n";
# Assigning 3 frames for the forward strand
for ($i=0; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame1 .=$codon;
}
for ($i=1; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame2 .=$codon;
}
for ($i=2; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame3 .=$codon;
}
# Assigning 3 frames for the reverse complementary strand
$revcom = reverse($dna);
$revcom =~ tr/AaTtGgCc/TtAaCcGg/;
for ($i=0; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame4 .=$codon;
}
for ($i=1; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame5 .=$codon;
}
for ($i=2; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame6 .=$codon;
}
print "Frame1: $frame1 \nFrame2: $frame2 \nFrame3: $frame3 \nFrame4: $frame4 \nFrame5: $frame5 \nFrame6: $frame6 \n" ;
@frames_array=($frame1,$frame2,$frame3,$frame4,$frame5,$frame6);
# Perl assigns the first element of the array at 0th position
for($i=0; $i<6; $i++)
{
# Match ATG-> START codon, then match at least 50 nucleotides, then match either of (TAA|TAG|TGA)-> STOP codons,
# g-> globally, i-> case insensitive. This match finds the first ATG and the last STOP codon in the frame.
if ($frames_array[$i] =~ m/(ATG)(.{50,})(TAA|TAG|TGA)/gi)
{
# $1 stands for (ATG), $2 stands for (.{50,}), $3 stands for (TAA|TAG|TGA)
$orf = $1.$2.$3;
$j = $i+1;
print "\n ORF found at Frame$j : $orf \n";
}
}
use strict;
my ($file,$line,$dna,$revcom,$i,$codon,@frames_array,$j,$orf);
my ($frame1,$frame2,$frame3,$frame4,$frame5,$frame6)='';
print "Enter the filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or
die "Cannot open file : $file \n\n";
while ($line = <FILE>)
{
if ($line =~ /^#/ )
{ next; }
elsif($line =~ /^>/ )
{ next; }
else
{ $dna .= $line; }
}
$dna =~ s/\s//g ;
close FILE;
print "Original Sequence is: $dna \n";
# Assigning 3 frames for the forward strand
for ($i=0; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame1 .=$codon;
}
for ($i=1; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame2 .=$codon;
}
for ($i=2; $i<length($dna)-2; $i+=3)
{
$codon = substr($dna,$i,3);
$frame3 .=$codon;
}
# Assigning 3 frames for the reverse complementary strand
$revcom = reverse($dna);
$revcom =~ tr/AaTtGgCc/TtAaCcGg/;
for ($i=0; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame4 .=$codon;
}
for ($i=1; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame5 .=$codon;
}
for ($i=2; $i<length($revcom)-2; $i+=3)
{
$codon = substr($revcom,$i,3);
$frame6 .=$codon;
}
print "Frame1: $frame1 \nFrame2: $frame2 \nFrame3: $frame3 \nFrame4: $frame4 \nFrame5: $frame5 \nFrame6: $frame6 \n" ;
@frames_array=($frame1,$frame2,$frame3,$frame4,$frame5,$frame6);
# Perl assigns the first element of the array at 0th position
for($i=0; $i<6; $i++)
{
# Match ATG-> START codon, then match at least 50 nucleotides, then match either of (TAA|TAG|TGA)-> STOP codons,
# g-> globally, i-> case insensitive. This match finds the first ATG and the last STOP codon in the frame.
if ($frames_array[$i] =~ m/(ATG)(.{50,})(TAA|TAG|TGA)/gi)
{
# $1 stands for (ATG), $2 stands for (.{50,}), $3 stands for (TAA|TAG|TGA)
$orf = $1.$2.$3;
$j = $i+1;
print "\n ORF found at Frame$j : $orf \n";
}
}

by binu at 04-24-2017, 05:38 PM
0 comments
#!/usr/bin/perl -w
use strict;
my ($file,$line,$sequence,$i,$codon,$CODON,$protein);
my %genetic_code = qw(
TTT F
TCT S
TAT Y
TGT C
TTC F
TCC S
TAC Y
TGC C
TTA L
TCA S
TAA _
TGA _
TTG L
TCG S
TAG _
TGG W
CTT L
CCT P
CAT H
CGT R
CTC L
CCC P
CAC H
CGC R
CTA L
CCA P
CAA Q
CGA R
CTG L
CCG P
CAG Q
CGG R
ATT I
ACT T
AAT N
AGT S
ATC I
ACC T
AAC N
AGC S
ATA I
ACA T
AAA K
AGA R
ATG M
ACG T
AAG K
AGG R
GTT V
GCT A
GAT D
GGT G
GTC V
GCC A
GAC D
GGC G
GTA V
GCA A
GAA E
GGA G
GTG V
GCG A
GAG E
GGG G
);
print "Enter the filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or die "Cannot open file : $file \n\n";
# if there are 10 lines in the file then while loop iterates 10 times
# next command resets the while loop to the next line
while ($line = <FILE>)
{
# Discard blank lines
if ($line =~ /^\s*#/ )
{ next; }
# Discard comment line
elsif ($line=~/^#/)
{ next; }
# Discard fasta header line
elsif($line =~ /^>/ )
{ next; }
# Keep concatenating to $sequence string
else
{ $sequence .= $line; }
}
$sequence =~ s/\s//g ;
close FILE;
for ($i=0; $i < (length ($sequence) - 2) ; $i += 3)
{
# From the string '$sequence' at position '$i' extract 3 characters & store it in '$codon'
$codon = (substr($sequence,$i,3));
# Converting any lower case characters to upper case
$CODON = uc $codon;
# Checking for the existence of CODON in the hash %genetic_code
if(exists $genetic_code{$CODON})
# The corresponding amino acid in the hash is stored in $protein
{ $protein .= $genetic_code{$CODON}; }
else
{ die "Bad codon !! \n\n";}
}
print "The translated protein sequence is : $protein \n\n";
use strict;
my ($file,$line,$sequence,$i,$codon,$CODON,$protein);
my %genetic_code = qw(
TTT F
TCT S
TAT Y
TGT C
TTC F
TCC S
TAC Y
TGC C
TTA L
TCA S
TAA _
TGA _
TTG L
TCG S
TAG _
TGG W
CTT L
CCT P
CAT H
CGT R
CTC L
CCC P
CAC H
CGC R
CTA L
CCA P
CAA Q
CGA R
CTG L
CCG P
CAG Q
CGG R
ATT I
ACT T
AAT N
AGT S
ATC I
ACC T
AAC N
AGC S
ATA I
ACA T
AAA K
AGA R
ATG M
ACG T
AAG K
AGG R
GTT V
GCT A
GAT D
GGT G
GTC V
GCC A
GAC D
GGC G
GTA V
GCA A
GAA E
GGA G
GTG V
GCG A
GAG E
GGG G
);
print "Enter the filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or die "Cannot open file : $file \n\n";
# if there are 10 lines in the file then while loop iterates 10 times
# next command resets the while loop to the next line
while ($line = <FILE>)
{
# Discard blank lines
if ($line =~ /^\s*#/ )
{ next; }
# Discard comment line
elsif ($line=~/^#/)
{ next; }
# Discard fasta header line
elsif($line =~ /^>/ )
{ next; }
# Keep concatenating to $sequence string
else
{ $sequence .= $line; }
}
$sequence =~ s/\s//g ;
close FILE;
for ($i=0; $i < (length ($sequence) - 2) ; $i += 3)
{
# From the string '$sequence' at position '$i' extract 3 characters & store it in '$codon'
$codon = (substr($sequence,$i,3));
# Converting any lower case characters to upper case
$CODON = uc $codon;
# Checking for the existence of CODON in the hash %genetic_code
if(exists $genetic_code{$CODON})
# The corresponding amino acid in the hash is stored in $protein
{ $protein .= $genetic_code{$CODON}; }
else
{ die "Bad codon !! \n\n";}
}
print "The translated protein sequence is : $protein \n\n";

by binu at 04-24-2017, 05:34 PM
0 comments
#!/usr/bin/perl -w
# Perl programs to find reverse complement, to perform transcription, to convert the DNA to binary form,
# To count the nucleotides, Mutate the DNA, Find the percent identity.
use strict;
my ($file,$line,$dna,$revcom,$rna,$binary,$pos,$newbase,$i,$mutant,$position);
my ($a,$g,$t,$c,$basecount,$nonbase,$percent_ag,$percent_identity,$count) = 0 ;
my @nucs = ('A', 'C', 'G', 'T');
# Ask the user for the fasta filename
print "Enter the fasta filename: ";
$file = <STDIN>;
# Remove the newline from the fasta filename
chomp $file;
# Open the file or exit
open (FILE,$file) or die "Cannot open file : $file \n\n";
# Each line in the file is operated only once by the while loop
# If there are 10 lines in the file then while loop iterates 10 times
# next command tells the while loop to go to the next line
while ($line = <FILE>)
{
# Discard blank lines
if ($line =~ /^\s*$/)
{ next; }
# Discard comment line
elsif ($line=~/^#/)
{ next; }
# Discard fasta header line
elsif ($line=~/^>/)
{ next; }
# Keep concatenating to $dna string
else
{ $dna .= $line; }
}
# Remove whitespaces
$dna =~ s/\s//g;
close FILE;
# Print the extracted nucleotide sequence
print "\nHere is the original DNA : $dna \n\n";
# To find the reverse complement
$revcom = reverse($dna);
# Transliterate operator converts each character individually
$revcom =~ tr/ACGTacgt/TGCAtgca/ ;
print "The reverse complement is : $revcom \n\n";
# To perform transcription
$rna = $dna;
# Substitute operator is used
$rna =~ s/T/U/g;
print "The transcribed RNA is : $rna \n\n";
# To convert the DNA to binary form
$binary = $dna;
#Purine(A,G)--> 1, Pyrimidine(T,C)--> 0
$binary =~ tr/ATGCatgc/10101010/ ;
print "The converted binary format is : $binary \n\n" ;
# To count the nucleotides
$a = ($dna =~ tr/Aa// ) ;
$t = ($dna =~ tr/Tt// ) ;
$g = ($dna =~ tr/Gg// ) ;
$c = ($dna =~ tr/Cc// ) ;
$basecount = ($dna =~ tr/ATGCatgc// ) ;
$nonbase = length ($dna) - $basecount ;
$percent_ag = (($a+$g)/($basecount)*100);
print "Nucleotide Count : \n" ;
print " A=$a \n T=$t \n G=$g \n C=$c \n Total Bases=$basecount \n Errors=$nonbase \n Purine Percentage=$percent_ag \n\n";
# Mutate the DNA 100 times
$mutant = $dna;
for ($i=1 ; $i <= 100 ; $i++)
{
# $pos stores an integer random number between 0 and [(length of $mutant)-1]
$pos = int rand length $mutant;
do
# To select at random one of the four nucleotides.
# [rand @nucs] returns a random integer (0,1,2,3) as there are 4 nucleotides.
{ $newbase = $nucs[rand @nucs];
}
# Make sure it's different from the nucleotide we're mutating. 'ne' stands for not equal to
until ($newbase ne substr($mutant,$pos,1));
# Insert the random nucleotide '$newbase' into the random position '$pos' in the mutant
# In the string '$mutant' at position '$pos' change 1 character to the string in '$newbase'
substr($mutant,$pos,1,$newbase);
}
print "The mutant DNA is : $mutant \n\n";
# Finding the percent identity between input DNA & mutant DNA
for ($position=0; $position < length($mutant) ; $position++)
{
# Match the input DNA with mutant DNA from first position
if(substr($dna,$position,1) eq substr($mutant,$position,1))
{ $count++; }
}
$percent_identity = ($count / (length($mutant)))*100;
print "There are $count identical nucleotides \n";
print "Percent Identity between input DNA & mutant DNA is : $percent_identity \n\n";
# Perl programs to find reverse complement, to perform transcription, to convert the DNA to binary form,
# To count the nucleotides, Mutate the DNA, Find the percent identity.
use strict;
my ($file,$line,$dna,$revcom,$rna,$binary,$pos,$newbase,$i,$mutant,$position);
my ($a,$g,$t,$c,$basecount,$nonbase,$percent_ag,$percent_identity,$count) = 0 ;
my @nucs = ('A', 'C', 'G', 'T');
# Ask the user for the fasta filename
print "Enter the fasta filename: ";
$file = <STDIN>;
# Remove the newline from the fasta filename
chomp $file;
# Open the file or exit
open (FILE,$file) or die "Cannot open file : $file \n\n";
# Each line in the file is operated only once by the while loop
# If there are 10 lines in the file then while loop iterates 10 times
# next command tells the while loop to go to the next line
while ($line = <FILE>)
{
# Discard blank lines
if ($line =~ /^\s*$/)
{ next; }
# Discard comment line
elsif ($line=~/^#/)
{ next; }
# Discard fasta header line
elsif ($line=~/^>/)
{ next; }
# Keep concatenating to $dna string
else
{ $dna .= $line; }
}
# Remove whitespaces
$dna =~ s/\s//g;
close FILE;
# Print the extracted nucleotide sequence
print "\nHere is the original DNA : $dna \n\n";
# To find the reverse complement
$revcom = reverse($dna);
# Transliterate operator converts each character individually
$revcom =~ tr/ACGTacgt/TGCAtgca/ ;
print "The reverse complement is : $revcom \n\n";
# To perform transcription
$rna = $dna;
# Substitute operator is used
$rna =~ s/T/U/g;
print "The transcribed RNA is : $rna \n\n";
# To convert the DNA to binary form
$binary = $dna;
#Purine(A,G)--> 1, Pyrimidine(T,C)--> 0
$binary =~ tr/ATGCatgc/10101010/ ;
print "The converted binary format is : $binary \n\n" ;
# To count the nucleotides
$a = ($dna =~ tr/Aa// ) ;
$t = ($dna =~ tr/Tt// ) ;
$g = ($dna =~ tr/Gg// ) ;
$c = ($dna =~ tr/Cc// ) ;
$basecount = ($dna =~ tr/ATGCatgc// ) ;
$nonbase = length ($dna) - $basecount ;
$percent_ag = (($a+$g)/($basecount)*100);
print "Nucleotide Count : \n" ;
print " A=$a \n T=$t \n G=$g \n C=$c \n Total Bases=$basecount \n Errors=$nonbase \n Purine Percentage=$percent_ag \n\n";
# Mutate the DNA 100 times
$mutant = $dna;
for ($i=1 ; $i <= 100 ; $i++)
{
# $pos stores an integer random number between 0 and [(length of $mutant)-1]
$pos = int rand length $mutant;
do
# To select at random one of the four nucleotides.
# [rand @nucs] returns a random integer (0,1,2,3) as there are 4 nucleotides.
{ $newbase = $nucs[rand @nucs];
}
# Make sure it's different from the nucleotide we're mutating. 'ne' stands for not equal to
until ($newbase ne substr($mutant,$pos,1));
# Insert the random nucleotide '$newbase' into the random position '$pos' in the mutant
# In the string '$mutant' at position '$pos' change 1 character to the string in '$newbase'
substr($mutant,$pos,1,$newbase);
}
print "The mutant DNA is : $mutant \n\n";
# Finding the percent identity between input DNA & mutant DNA
for ($position=0; $position < length($mutant) ; $position++)
{
# Match the input DNA with mutant DNA from first position
if(substr($dna,$position,1) eq substr($mutant,$position,1))
{ $count++; }
}
$percent_identity = ($count / (length($mutant)))*100;
print "There are $count identical nucleotides \n";
print "Percent Identity between input DNA & mutant DNA is : $percent_identity \n\n";

by binu at 04-24-2017, 05:29 PM
0 comments
PAPER 2 - THEORY
A question paper containing 55 questions (10 pages) is provided. A separate answer sheet (30 pages) to answer 20 questions is given. Each 10 mark answer needs to be written on one side of a page only. Each question is of 10 marks. The marks subdivisions are: 5+5, 6+4, 7+3, 4+3+3, 10.
SECTION - A
Bioinformatics :
1. What is Molecular dynamic simulation. How is temperature increased.
2. Draw Ramachandran plot. Allowed and disallowed regions.
3. Ramachandran plot. Steric hindrance and angles.
4. Amino acids- polar, non-polar, hydrophobic, hydrophilic, aromatic, positive, negative. Why are there some exceptions.
5. QSAR. Pharmacophore model.
6. Docking- rigid flexible semi-flexible. Ligand based drug designing.
7. Monte carlo docking. Structure based drug design.
8. Array express DB. Synonymous SNP vs non synonymous. Role in evolution.
9. Protein threading method.
10. Artificial neural networks. Higher orders (BRNN). Use in secondary structure prediction.
11. Supervised vs unsupervised learning with example.
12. 2d page numerical
13. Fastq format. Something else
14. Flux balance analysis.
15. Rnaseq vs dnaseq.
16. KEGG database. Something else
17. Numerical on dna microarray
18. Numerical on gene expression
19. Denovo assembly
20. Boolean network simulation
21. Leonard jones potential numerical
22. Force field calculation due to torsion angles numerical
23. Gene regulatory networks.
24.
25.
SECTION - B
Biology :
1. Competitive vs non competitive inhibition with diagram and LB plot.
2. Promoter, enhancer, locus region.
3. Operon model. Gene expression
4. Mitochondrial dna related to maternal inheritance.
5. Isozymes. Examples. Something else.
Chemistry:
6. Dissociation constant numerical
7. Bohrs radius numerical
8. Calculate ph.
9. Endergonic vs exergonic reaction. Relation with free energy.
10.
Physics:
11. Fluorescence numerical
12. Enzyme kinetics numerical
13.
14.
15.
SECTION - C
Information Technology :
1. NoSQL merits demerits. GET POST methods in CGI.
2. Pseudocode of adding 2 n*n matrices, the sum of rows and columns of resultant matrix.
3. Program to input 3 words. Calculate vowels and consonants. Toggle upper case lower case. Replace all vowels with x.
4. Program : Result file is provided. 3 columns are : name, roll no, marks. Take marks column. Find the highest and lowest marks. Find average marks.
5. Create table. Perform some operations. Bubble sort algorithm.
Maths :
6. Solve 2nd order linear differential equation.
7. Matrix ‘A’ and inverse matrix given. Find value of : A^2 + 2A + ....
8. Calculate mean and variance of first n natural numbers. Population variance and...
9. Vector numerical.
10. Eigen vector calculation.
Statistics :
11. Binomial distribution numerical
12. Poisson distribution numerical
13. Null hypothesis numerical
14. Markov chain numerical
15. Testing of hypothesis numericalPAPER 3 - Programming
1a. Intra Molecular Distance Matrix calculation (50 marks) : ATOM lines (155) of a pdb file are provided in input file (only C@ residues). Calculate intra molecular distance between each C@ residue. If distance >= 6, print 1 in distance matrix of output file, else print 0 in distance matrix. Comment on the secondary structures present.
1b. Chou fasman prediction (50 marks) : Amino acid sequence (50 residues) is provided in input file. Extract it. Make octamers of amino acids from the file and calculate their alpha and beta propensity by using second input file. Eg. - 1-8, 2-9, 3-10,....till 50. Second input file contains 20 amino acids with their alpha and beta propensity values in 3 columns. Parse through it using array or store it in a hash. Print the resultant alpha, beta propensity scores for each octamer in output file.
OR
2a. Distance calculation (60 marks) : ATOM lines of a pdb file are provided in input file. Calculate distance between backbone amino acid and side chains. Many other questions were also there.
2b. Gene silencing (40 marks) : mRNA sequence is provided in first input file. miRNA sequences(3) are provided in second input file. Find when gene silencing will occur.

by binu at 04-24-2017, 05:03 PM
2 comments
BIOINFORMATICS - 30 questions
1. STRING does not calculate.
2. Gibbs law representation in mathematical form.
3. Protein-Protein Interactions
4. GEO data set refers to : single set of experiment, single GEO organism,...
5. Zinc is used in X-ray Crystallography for : Phase correction, Stability,...
6. Haemophilia is : X-linked recessive Homolgy trait, Y-linked,...
7. Amino Acid exists in : Neutral & zwitter ionic form, Positive & Negative form,...
8. Silent Mutations caused by : Frameshift, Codon replacement
9. Single continuous diagonal line in dot plot shows : 100% similarity, 80%, 50%, 20%
10. Proteins which do not fold correctly are : discarded, sent back for repair to ribosome, ...
11. In X-ray Crystallography high resolution refers to : lower atomic distance, higher size of crystals, ...
12. AMBER used in : Molecular Dynamic Simulation,...
13. Amino Acids other than 20 are called : Non-Standard, Mutated, Modified Residues,.
14. Homology Modeling is based on : Similarity, ...
15. Phi,Psi for @-helix : 60-40, 60-100, ...
16. RMSD high means : lower similarity in structure, lower similarity in alignment,...
17. Calculate sequence identity by pairwise alignment between 2 given sequences
18. Molecular Dynamic Simulations time used : 2 ns, 10 ns, 2 femtosec, 10 femtosec
19. Masking refers to : LCR,...
20. PDB atom distances given in : ATOM lines, ...
21. NOT a Genome browser : UCSC, DALI, EMBOSS, ...
22. Which is best for aligning sequences : BLAST, PSIBLAST, Needleman-Wunsch,...
23. G-C more stable than A-T because of : 3 hydrogen bonds,...
24. SNP means
25. Primary Structure of protein stabilised by : Covalent, Ionic, Hydrogen bonding, van der Waals.
26. BLOSUM full form
27. Which cause kink in @-helix : Proline, Alanine, ...
28. High G-C content refers to : promoter presence
29. Oligoprotein of single chain : quaternary, tertiary, secondary.
30. Energy depends on : inverse of square of distane between 2 charged particles, inverse of distane , directly proportional,..
Biology - 20 questions
1. RNA editing
2. Restriction Endonuclease
3. Protection of mRNA by : Capping, Tailing,...
4. Vaccine related
5. Intron not present in : Bacteria, Fish, Plant, Fruit fly.
6. Bending DNA domain : double stranded, single stranded,...
7. Semi Conservative Replication means
8. Alternative Splicing done for exons : 75%, 50%, 20%, 100%
9. C-value contains - haploid, diploid,...
10. mitochondrial RNA property
11. Telomeres are present at : middle of chromosome, end of chromosome,...
Physics - 8 questions
1. Gibbs free energy
2. Force is dependent on : inverse of square of distance between 2 particles
3. Potential Energy is dependent on : distance between 2 objects, ...
4. Calculate Force? mass & acceleration given
5. Calculate difference in momentum? velocity difference given
6. Calculate acceleration? speed & distance values provided
7. Calculate acceleration? velocity & time values provided
8. What happens when distance between 2 charged particles is doubled : related to force.
Chemistry - 7 questions
1. Calculate pH of 0.05M HCL
2. Free energy : positive, negative means spontaneous reaction
3. Relation between Boltzman constant, Gas Constant, Avogadro number : R=Nk,...
4. Bent structure of water due to : lone pair of electrons, H-atoms attract each other,...
5. Law of Conservation of Energy : Newton's first law, Second law of thermodynamics,..
6. Entropy of system : closed system, open system,...
7. Enthalpy related
Maths - 8 questions
1. Differentiation
2. Differentiation
3. Matrix (a*b)(b*c) : b[a b c], a[a b c], c[a b c],...
4. Inverse of matrix can be found when : |A| !=0, adj A = 0,...
5. Equation of straight line passing through a point
6. Equation of ellipse passing through 2 points
7. Probability
8. Find maxima of function
Statistics - 7 questions
1. Continuous random variable equation given. Find maxima
2. Find maxima of function
3. Find maxima of function
4. Find maxima of function
5. Poisson distribution
6. Poisson distribution
7. Binomial distribution
Information Technology - 20 questions
1. Which of them always occur together : (Group by,having), (Commit,Rollback),...
2. Operator performs on operand
3. Which OS is time sharing : Linux, DOS,...
4. STAR, BUS, Mesh Topology
5. MongoDB is : NoSQL, RDBMS, DBMS,...
6. who | wc -1 output will be : number of users logged in ,...
7. Piping use
8. grep use
9. Command for renaming : mv, ren, rename,...
10. Encapsulation definition given in question
11. Inheritance example
12. Which is called implicitly when class instance is invoked : Constructor, Destructor,...
13. DML statements : Select Insert Update Delete,...
14. Shell function
15. Kernel function
16. Tuple in DBMS refers to : row in table, column in table,...
17. Which is volatile memory : RAM, ROM, Hard disk, pen drive
18. Geographically separated : MAN,WAN,LAN
19. Operating System Function
20. Scope signifies
1. STRING does not calculate.
2. Gibbs law representation in mathematical form.
3. Protein-Protein Interactions
4. GEO data set refers to : single set of experiment, single GEO organism,...
5. Zinc is used in X-ray Crystallography for : Phase correction, Stability,...
6. Haemophilia is : X-linked recessive Homolgy trait, Y-linked,...
7. Amino Acid exists in : Neutral & zwitter ionic form, Positive & Negative form,...
8. Silent Mutations caused by : Frameshift, Codon replacement
9. Single continuous diagonal line in dot plot shows : 100% similarity, 80%, 50%, 20%
10. Proteins which do not fold correctly are : discarded, sent back for repair to ribosome, ...
11. In X-ray Crystallography high resolution refers to : lower atomic distance, higher size of crystals, ...
12. AMBER used in : Molecular Dynamic Simulation,...
13. Amino Acids other than 20 are called : Non-Standard, Mutated, Modified Residues,.
14. Homology Modeling is based on : Similarity, ...
15. Phi,Psi for @-helix : 60-40, 60-100, ...
16. RMSD high means : lower similarity in structure, lower similarity in alignment,...
17. Calculate sequence identity by pairwise alignment between 2 given sequences
18. Molecular Dynamic Simulations time used : 2 ns, 10 ns, 2 femtosec, 10 femtosec
19. Masking refers to : LCR,...
20. PDB atom distances given in : ATOM lines, ...
21. NOT a Genome browser : UCSC, DALI, EMBOSS, ...
22. Which is best for aligning sequences : BLAST, PSIBLAST, Needleman-Wunsch,...
23. G-C more stable than A-T because of : 3 hydrogen bonds,...
24. SNP means
25. Primary Structure of protein stabilised by : Covalent, Ionic, Hydrogen bonding, van der Waals.
26. BLOSUM full form
27. Which cause kink in @-helix : Proline, Alanine, ...
28. High G-C content refers to : promoter presence
29. Oligoprotein of single chain : quaternary, tertiary, secondary.
30. Energy depends on : inverse of square of distane between 2 charged particles, inverse of distane , directly proportional,..
Biology - 20 questions
1. RNA editing
2. Restriction Endonuclease
3. Protection of mRNA by : Capping, Tailing,...
4. Vaccine related
5. Intron not present in : Bacteria, Fish, Plant, Fruit fly.
6. Bending DNA domain : double stranded, single stranded,...
7. Semi Conservative Replication means
8. Alternative Splicing done for exons : 75%, 50%, 20%, 100%
9. C-value contains - haploid, diploid,...
10. mitochondrial RNA property
11. Telomeres are present at : middle of chromosome, end of chromosome,...
Physics - 8 questions
1. Gibbs free energy
2. Force is dependent on : inverse of square of distance between 2 particles
3. Potential Energy is dependent on : distance between 2 objects, ...
4. Calculate Force? mass & acceleration given
5. Calculate difference in momentum? velocity difference given
6. Calculate acceleration? speed & distance values provided
7. Calculate acceleration? velocity & time values provided
8. What happens when distance between 2 charged particles is doubled : related to force.
Chemistry - 7 questions
1. Calculate pH of 0.05M HCL
2. Free energy : positive, negative means spontaneous reaction
3. Relation between Boltzman constant, Gas Constant, Avogadro number : R=Nk,...
4. Bent structure of water due to : lone pair of electrons, H-atoms attract each other,...
5. Law of Conservation of Energy : Newton's first law, Second law of thermodynamics,..
6. Entropy of system : closed system, open system,...
7. Enthalpy related
Maths - 8 questions
1. Differentiation
2. Differentiation
3. Matrix (a*b)(b*c) : b[a b c], a[a b c], c[a b c],...
4. Inverse of matrix can be found when : |A| !=0, adj A = 0,...
5. Equation of straight line passing through a point
6. Equation of ellipse passing through 2 points
7. Probability
8. Find maxima of function
Statistics - 7 questions
1. Continuous random variable equation given. Find maxima
2. Find maxima of function
3. Find maxima of function
4. Find maxima of function
5. Poisson distribution
6. Poisson distribution
7. Binomial distribution
Information Technology - 20 questions
1. Which of them always occur together : (Group by,having), (Commit,Rollback),...
2. Operator performs on operand
3. Which OS is time sharing : Linux, DOS,...
4. STAR, BUS, Mesh Topology
5. MongoDB is : NoSQL, RDBMS, DBMS,...
6. who | wc -1 output will be : number of users logged in ,...
7. Piping use
8. grep use
9. Command for renaming : mv, ren, rename,...
10. Encapsulation definition given in question
11. Inheritance example
12. Which is called implicitly when class instance is invoked : Constructor, Destructor,...
13. DML statements : Select Insert Update Delete,...
14. Shell function
15. Kernel function
16. Tuple in DBMS refers to : row in table, column in table,...
17. Which is volatile memory : RAM, ROM, Hard disk, pen drive
18. Geographically separated : MAN,WAN,LAN
19. Operating System Function
20. Scope signifies

by binu at 04-24-2017, 04:53 PM
0 comments
BINC 2016 part 1- MCQs
BioInformatics - 40 questions
1) Which is better - mid-point rooting,outgroup,...
2) How many branches converge at node in tree - 1,2,3,4
3) Rooted tree is given - which taxa are closer to each other
4) Simplest Nucleotide Substitution model - Jukes Cantor,Kimura,....
5) Salt bridges occur between - positive-negative charges,...
6) Why is B-sheet difficult to predict -
7) What is iterated in PSI-BLAST - PSSM,Z-score,E-value,...
8) Which is distance based - Neighbour Joining,Maximum Parsimony,...
9) Causes of overfitting - similar sequences,...
10) Neutral Evolution theory
11) Flux Balance Analysis
12) Flux Balance Analysis
13) Two divergent sequences parallel evolution - Heterosis, Homonomy, Homology, ..
14) Leave-one-out, n-fold theory
15) Coevolution, concerted evolution, Microevolution, ..
16) Artemis - Genome comparison, DNA sequence comparison,...
17) Which is better comparison - Profile vs Profile, Sequence vs Sequence, Profile vs Sequence
18) Bidirectional best hits used in - COG, PDB,....
19) Exon related - it is used
20) Intron related - it is removed
21) H-index used in publications
22) Which step is not there in shotgun sequencing - cloning, sequencing,...
23) PCR related
24) Some scientist used some method to find something - Column chromatography, Electrophoresis,..
25) Chip-seq experiment
26) PFAM made of - profiles, sequences, ...
27) UniGene
28) 7 chain amino acid given - identify by polarity,hydrophobicity, basicity, acidity
29) Non-mutable Amino acid - cysteine,...
30) PAM30, PAM70 some comparison
31) SNP
32) protein homology best shown by - TBLASTX, BLASTP
33) PSSM
34) When to use - BLASTP, TBLASTX, BLASTX
35) 5 questions on E-value, Z-score, P-value - what will happen when one increases, database dependency, similarity, 2 small sequences should be compared by.
till 40
Biology - 20 questions
1) Histones composed of - arginine+lysine, histidine,..
2) Common compound in Glycolysis, Krebbs Cycle.... - Acetyl CoA, pyruvate,...
3) Blood Group Genotypes - 2,3,4,5
4) Pleiotropic gene
5) Where is X seen - Anaphase, prophase, cytokinesis, metaphase
6) Proofreading activity - 5'-3' polymerase activity, 5'-3' exonuclease activity, 3'-5' polymerase activity, 3'-5' ..
7) Phosphofructokinase, polymerase
8) Which is false about Lac operon - negative control, repressor binds to promoter,..
9) Lipid action find false - lipid acts as hormone, all cell membranes contain lipids,..
10) Allosteric Enzyme
11) Allosteric Enzyme
Maths - 5 questions
1) 1 circle inside large circle sharing similar radius-diameter - find shaded area.
2) 2 circles inside large circle - find excluded area
3) probability value can't be negative
4) set theory - 70 people like A, 30 people like B, 10 people like both, total 100 people, how many do not like anything.
5) find wrong notation - sin (inverse) x, sin x(inverse), (sin x) inverse,...
Statistics - 5 questions
1) Binomial Distribution
2) Binomial Distribution
3) Poisson Distribution
4) Poisson Distribution
5) Binomial vs Poisson Distribution
Physics - 5 questions
1) Energy Dimension - MLT,...
2) First Law of Thermodynamics contains - Entropy, Enthalpy, Energy, ..
3) Calculate momentum - values given
4) Carnot engine efficiency, find temperature @ 30% efficiency - values given
5) Enthalpy related
Chemistry - 5 questions
1) Find quantum number for Bohr Radius - values provided
2) Adsorption of hydrogen on platinum - exothermic. endothermic,..
3) Diamond structure - carbon bonds
4) Respiration equation - 1 oxygen molecule gives 1 carbon dioxide
5) Water - specific heat, heat of formation,...
Information Technology - 20 questions
1) kernel, connector, shell
2) line starts with - symbol, root,..
3) grep -v -c
4) grep head -20
5) grep computer$ will find
6) Unix error direction - >>,<<,>,<
7) Not a logical operator - >>,>,=,..
8) Number of operands required in ? operator - 1,2,3,4
9) if statement with logical inputs provided
10) AND operator provides output only when both inputs are true
11) Key value pair in Perl - hash, array,...
12) Not OOP - C,Java,Python,C++
13) Which is the most significant digit in Hexadecimal system
14) DCL statements
15) Class in Java preceded by
16) Operator Overloading example
17) Constructor, Destructor
18)
19)
20)
BioInformatics - 40 questions
1) Which is better - mid-point rooting,outgroup,...
2) How many branches converge at node in tree - 1,2,3,4
3) Rooted tree is given - which taxa are closer to each other
4) Simplest Nucleotide Substitution model - Jukes Cantor,Kimura,....
5) Salt bridges occur between - positive-negative charges,...
6) Why is B-sheet difficult to predict -
7) What is iterated in PSI-BLAST - PSSM,Z-score,E-value,...
8) Which is distance based - Neighbour Joining,Maximum Parsimony,...
9) Causes of overfitting - similar sequences,...
10) Neutral Evolution theory
11) Flux Balance Analysis
12) Flux Balance Analysis
13) Two divergent sequences parallel evolution - Heterosis, Homonomy, Homology, ..
14) Leave-one-out, n-fold theory
15) Coevolution, concerted evolution, Microevolution, ..
16) Artemis - Genome comparison, DNA sequence comparison,...
17) Which is better comparison - Profile vs Profile, Sequence vs Sequence, Profile vs Sequence
18) Bidirectional best hits used in - COG, PDB,....
19) Exon related - it is used
20) Intron related - it is removed
21) H-index used in publications
22) Which step is not there in shotgun sequencing - cloning, sequencing,...
23) PCR related
24) Some scientist used some method to find something - Column chromatography, Electrophoresis,..
25) Chip-seq experiment
26) PFAM made of - profiles, sequences, ...
27) UniGene
28) 7 chain amino acid given - identify by polarity,hydrophobicity, basicity, acidity
29) Non-mutable Amino acid - cysteine,...
30) PAM30, PAM70 some comparison
31) SNP
32) protein homology best shown by - TBLASTX, BLASTP
33) PSSM
34) When to use - BLASTP, TBLASTX, BLASTX
35) 5 questions on E-value, Z-score, P-value - what will happen when one increases, database dependency, similarity, 2 small sequences should be compared by.
till 40
Biology - 20 questions
1) Histones composed of - arginine+lysine, histidine,..
2) Common compound in Glycolysis, Krebbs Cycle.... - Acetyl CoA, pyruvate,...
3) Blood Group Genotypes - 2,3,4,5
4) Pleiotropic gene
5) Where is X seen - Anaphase, prophase, cytokinesis, metaphase
6) Proofreading activity - 5'-3' polymerase activity, 5'-3' exonuclease activity, 3'-5' polymerase activity, 3'-5' ..
7) Phosphofructokinase, polymerase
8) Which is false about Lac operon - negative control, repressor binds to promoter,..
9) Lipid action find false - lipid acts as hormone, all cell membranes contain lipids,..
10) Allosteric Enzyme
11) Allosteric Enzyme
Maths - 5 questions
1) 1 circle inside large circle sharing similar radius-diameter - find shaded area.
2) 2 circles inside large circle - find excluded area
3) probability value can't be negative
4) set theory - 70 people like A, 30 people like B, 10 people like both, total 100 people, how many do not like anything.
5) find wrong notation - sin (inverse) x, sin x(inverse), (sin x) inverse,...
Statistics - 5 questions
1) Binomial Distribution
2) Binomial Distribution
3) Poisson Distribution
4) Poisson Distribution
5) Binomial vs Poisson Distribution
Physics - 5 questions
1) Energy Dimension - MLT,...
2) First Law of Thermodynamics contains - Entropy, Enthalpy, Energy, ..
3) Calculate momentum - values given
4) Carnot engine efficiency, find temperature @ 30% efficiency - values given
5) Enthalpy related
Chemistry - 5 questions
1) Find quantum number for Bohr Radius - values provided
2) Adsorption of hydrogen on platinum - exothermic. endothermic,..
3) Diamond structure - carbon bonds
4) Respiration equation - 1 oxygen molecule gives 1 carbon dioxide
5) Water - specific heat, heat of formation,...
Information Technology - 20 questions
1) kernel, connector, shell
2) line starts with - symbol, root,..
3) grep -v -c
4) grep head -20
5) grep computer$ will find
6) Unix error direction - >>,<<,>,<
7) Not a logical operator - >>,>,=,..
8) Number of operands required in ? operator - 1,2,3,4
9) if statement with logical inputs provided
10) AND operator provides output only when both inputs are true
11) Key value pair in Perl - hash, array,...
12) Not OOP - C,Java,Python,C++
13) Which is the most significant digit in Hexadecimal system
14) DCL statements
15) Class in Java preceded by
16) Operator Overloading example
17) Constructor, Destructor
18)
19)
20)