Bioinformatic Tools - Introduction
Bioinformatic tools are software programs
that are designed for extracting the meaningful information from the mass of
data & to carry out this analysis step.
Factors that must be taken into
consideration when designing these tools are:
The end user (the
biologist) may not be a frequent user of computer technology
These software tools
must be made available over the internet given the global distribution of the
scientific research community
Major categories of Bioinformatics Tools
There are both standard and customized products to meet the requirements of
particular projects. There are data-mining software that retrieve data from
genomic sequence databases and also visualization tools to analyze and
retrieve information from proteomic databases. These can be classified as
homology and similarity tools, protein functional analysis tools, sequence
analysis tools and miscellaneous tools. Here is a brief description of a few
of these Everyday bioinformatics is done with sequence search programs like
BLAST, sequence analysis programs, like the EMBOSS and Staden packages,
structure prediction programs like THREADER or PHD or molecular
imaging/modelling programs like RasMol and WHATIF.
Homology and Similarity Tools:
Homologous sequences are sequences that are
related by divergence from a common ancestor. Thus the degree of similarity
between two sequences can be measured while their homology is a case of being
either true of false. This set of tools can be used to identify similarities between
novel query sequences of unknown structure and function and database
sequences whose structure and function have been elucidated.
Protein Function Analysis:
This group of programs allow you to compare
your protein sequence to the secondary (or derived) protein databases that
contain information on motifs, signatures and protein domains. Highly
significant hits against these different pattern databases allow you to
approximate the biochemical function of your query protein.
This set of tools allow you to compare
structures with the known structure databases. The function of a protein is
more directly a consequence of its structure rather than its sequence with
structural homologs tending to share functions. The determination of a protein's
2D/3D structure is crucial in the study of its function.
This set of tools allows you to carry out
further, more detailed analysis on your query sequence including evolutionary
analysis, identification of mutations, hydropathy regions, CpG islands and
compositional biases. The identification of these and other biological
properties are all clues that aid the search to elucidate the specific
function of your sequence.
Some examples of Bioinformatics Tools:
BLAST (Basic Local Alignment Search Tool)
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.
Comparison of nucleotide sequences in a database can be performed. Also a
protein database can be searched to find a match against the queried protein
sequence. NCBI has also introduced the new queuing system to BLAST (Q BLAST)
that allows users to retrieve results at their convenience and format their
results multiple times with different formatting options.
Depending on the type of sequences to
compare, there are different programs:
blastp compares an
amino acid query sequence against a protein sequence database
blastn compares a
nucleotide query sequence against a nucleotide sequence database
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