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Bioinformatics Tools - Databases, Alignment, Evolutionary and Protein Analysis
#1
This is post no. 1 under the main topic.
Bioinformatics is a field where computational methods are used to unravel mysteries of biology. These computational methods could be anything from homology sequence analyzing to predicting the structure and function of a given sequence. Below are the tools that are mainly used in bioinformatics.

Databases- There are a number of databases available online for DNA, RNA and Proteins. Over the decade, the databases are being updated. The most commonly used databases are GENBANK, EMBL-EBI, and UNIPROT. Separate databases are now available for human, parasite, yeast etc.

Alignment tools-The tools which can be used for homology search and alignment includes BLAST, FASTA, SSearch, GL Search etc. The sequences can be uploaded as a file or to be submitted in fasta format. Multiple sequence alignments can be done by packages like MUSCLE, Clustal-W/X T-Coffee etc.

Functions of protein can be predicted from the conserved sequences of the known protein or the structure of the same which is because those sequences could be resulting from the gene conservation throughout the process of evolution. Tracing back the roots of evolution of these sequences which have similar function, reveals a common ancestor. But ‘moonlighting proteins’, the proteins which have dual functions are exceptions for these types of predictions. For e.g. Phosphoglucose isomerase, an enzyme catalyzing the formation of Fructose -6- phosphate from Glucose -6- phosphate in glycolysis acts as a cytokine outside the cell causing B cell maturation also acts as a growth factor for neurons.

To predict the function, the sequence has to be aligned against sequences in the database for identifying the best match, which could be either a domain or protein. These domains are responsible for the functionality of the protein. Match towards the domain reflects the functional similarity. Match towards an entire protein reflects the close relation between the query and the subject. If prediction is based on the structure, the structural comparison tools can be used.

Protein Analysis- Analysis of protein can be achieved either in the structural or in the functional level; various tools are available for the same, like CATH, SCOP, VAST, PPSEARCH etc. A new tool have been developed called Tempura, it predicts the function and compares the structure. Secondary and tertiary structures could be evaluated using tools like Scansite, Motif Scan, and COILS. Modelers like Swiss-model and Modeller enables the user to create a 2D, 3D model of the protein based on sequences.

Evolutionary analysis – It is an area where bioinformatics tools can be exploited to its core. Phylogenetic trees can be created based on several algorithms, like Maximum Parsimony, Neighbor Joining, UPGMA. Trees can be created using softwares like Phylip, Mega, PAUP etc. There are special programs to evaluate the evolutionary distance of an organism and compare the distances between organisms, based on the similarity and on the algorithm of choice the close related ones are grouped together. For genuineness of the tree bootstrapping can be employed.

The scope of Bioinformatics is huge in modern molecular biology studies. Only certain areas are mentioned here, where there are wide number of online tools as well as software packages available for analyzing the datas.
 
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#2
This is post no. 2 under the main topic.
Very interesting .. Just adding a couple more

Mascot, Profound and PeptIdent are additional tools for Peptide mass fingerprinting.
InterProScan is based on integrated search and used for searching protein function.
 
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#3
This is post no. 3 under the main topic.
These Bioinformatics tools information given by you is really nice,I really like all these information, well according to my point of view, I think that Bioinformatics tools are the software programs for the saving, retrieving and analysis of Biological data and extracting the information from them.
 
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#4
This is post no. 4 under the main topic.
BLAST comes under the category of homology and similarity tools. It is a set of search programs designed for the Windows platform and is used to
perform fast similarity searches regardless of whether the query is for protein or DNA.
 
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#5
This is post no. 5 under the main topic.
Here are some new and freely accessible biomedical databases:

Drug2Gene: It’s free and unifies a number of popular public resources to provide structured and organized information for identified and reported relations between genes/proteins and drugs/compounds. It allows user’s interactive management by the ability to flag, comment and update relations, to import new drug-gene relations valuable for a specific project. Gene orthology and similarity information is matched to certain relationship entries assisting the prediction of new unreported drug-gene associations. You can go to the original source of the reported relation and explore for more facts, details and evidences...
PhenomicDB: It's a free multi-organism phenotype-genotype data repository unifying a variety of primary sources to make phenotypic data from a wide range of species and model organisms simultaneously searchable, visible and comparable. Gene orthology and similarity information mapped to particular entries, and the phenotypic data clustering system, provide facilities for the discovery of new phenotypic manifestations of a given genotype. Reported genotype-phenotype relationships are supported by evidence and reference links.
Here is a free online tool for text extraction analysis (new functionalities are to be added):

WebRT: Metalife Web Recognition Tool is a light text mining tool developed for online text analysis of diverse-type biomedical and molecular biology literature contents. Its main function is terms/phrase extraction and categorization with the ability to recognize synonyms, acronyms and spelling variations, to normalize and unify hits, to distinguish between seemingly equal terms with different categorization, etc. Relations extraction is expected soon...
 
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#6
This is post no. 6 under the main topic.
Building on the recognition of the importance of information transmission, accumulation and processing in biological systems, in 1978 Paulien Hogeweg, coined the term "Bioinformatics" to refer to the study of information processes in biotic systems.[1] This definition placed bioinformatics as field parallel to biophysics and biochemistry. Examples of relevant biological information processes studied in the early days of bioinformatics are the formation of complex social interaction structures by simple behavioral rules, and the information accumulation and maintenance in models of prebiotic evolution.

At the beginning of the "genomic revolution", the term bioinformatics was re-discovered to refer to the creation and maintenance of a database to store biological information such as nucleotide sequences and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could access existing data as well as submit new or revised data.
 
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#7
This is post no. 7 under the main topic.
(10-04-2012, 04:47 PM)Thomast22 Wrote: Building on the recognition of the importance of information transmission, accumulation and processing in biological systems, in 1978 Paulien Hogeweg, coined the term "Bioinformatics" to refer to the study of information processes in biotic systems.[1] This definition placed bioinformatics as field parallel to biophysics and biochemistry. Examples of relevant biological information processes studied in the early days of bioinformatics are the formation of complex social interaction structures by simple behavioral rules, and the information accumulation and maintenance in models of prebiotic evolution.

At the beginning of the "genomic revolution", the term bioinformatics was re-discovered to refer to the creation and maintenance of a database to store biological information such as nucleotide sequences and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could access existing data as well as submit new or revised data.

We all know that biological research is a field which is an ongoing process. This has resulted in collection of huge information on biology subject and its developments. Now this data needs to be shared to prepare the knowledge bank which can serve as a tool for future progress. Bioinformatics is playing a good role in this. Data collection, its correlation, analysis and finding the application are mainly possible due to bioinformatics. New improvements in data collection are ongoing process and the challenge is to provide a way to store the data such that it is user-friendly with ability of compatibility with new upcoming ways of data storage. Much new software is now a day’s available for finding the data for specific genome or proteins like Nucleic Acids research database, proteomics database, metabolomics database, gene expression ways, Gene location in genome etc.
Today’s software in bioinformatics are not only user friendly but also have lot of database within the system which provide all option to create own user-friendly interface while working, like workflow systems, which provides user option of sharing the workflow and providing the results online. Galaxy, Taverna is the best examples of it. With the help of Bioinformatics data up to the level of prediction of gene sequence is possible, protein 3-Dimensional modeling with animation are being done in research fields, Also comparison of any cellular morphology with the other tissues of same or other species is easily done. One of the most uses of this database is being one protein engineering technique which provides all information at the time of research which reduces the time and is cost efficient.
 
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#8
This is post no. 8 under the main topic.
Bioinformatics is the science concerned with the development and application of computer hardware and software to the acquisition, storage, analysis and visualization of biological information.

A database is a vast collection of data pertaining to a specific topic, e.g., nucleotide sequence, protein sequence etc., in an electronic environment. Databases are the heart of bioinformatics. There are a very large number of databases, which is growing rapidly.
The utilization of various databases requires the use of suitable search engines and analysis tools. These tools are often called database mining tools and the process of database utilization is known as database mining.

BLAST (Basic Local Alignment Search Tool) is a family of user-friendly sequence similarity search tools on the web. The BLASt server is supported through NCBI, USA. This tool is designed to identify potential homologues for a given sequence. It can analyze both DNA and protein sequences. Identification of homologues allows the prediction of potential functions and in modeling of the 3-D structure. A local alignment finds the optimal alignment between sub regions or local regions of the specified sequences. A local alignment search tool is used to find sequence motifs, domains, etc.

There are several BLAST programmes. Each of them serves as specific purpose. The different types of BLAST programmes are briefly described below. The new BLAST programmes are called BLAST 2.0.

1. BLASTp. It compares the submitted protein sequence against a protein database.
2. BLASTx. This programmes translates the submitted nucleotide sequence into amino acid sequence and compares the latter with a protein database.
3. BLASTn. This is used to compare a nucleotide sequence with a nucleotide sequence database.
4. tBLASTn. The programme converts the submitted protein sequence into nucleotide sequence and compares it with nucleotide sequence database.
5. tBLASTx. This programme translates the submitted nucleotide sequence as well as the nucleotide sequence database into amino acid sequences and searches for homology between the two.

ENTREZ.
It is one of the most popular search engines at NCBI, USA. It searches bibliographic citations and biological data from a variety of reliable databases, viz., SWISS-PROT, PDB, GeneBank, and EMBL etc. It offers a variety of criteria of information, e.g., all possible citations from a given author that deal with a given subject that deal with a given subject, standard names for given genes, a given sequence database etc.
 
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#9
This is post no. 9 under the main topic.
If you have stumbled on this thread looking for databases or sources of human genomic data... Repositive has indexed metadata from 34 sources including, Horizon Discovery, Array Express, Xpressomics, EBI Metagenomics, Genome Asia, SRA, dbGAP, GEO, ExAC and many more.
 
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#10
This is post no. 10 under the main topic.
(11-10-2016, 09:43 PM)CraigRepositive Wrote: If you have stumbled on this thread looking for databases or sources of human genomic data... Repositive has indexed metadata from 34 sources including, Horizon Discovery, Array Express, Xpressomics, EBI Metagenomics, Genome Asia, SRA, dbGAP, GEO, ExAC and many more.

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