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Bioinformatics Tools - Databases, Alignment, Evolutionary and Protein Analysis
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.
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.
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.
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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