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Alignment / Similarity Search Tools
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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 allow 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:
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blastp : compares an amino acid query sequence against a protein sequence database
blastn : compares a nucleotide query sequence against a nucleotide sequence database
blastx : compares a nucleotide query sequence translated in all reading frames against a protein sequence database
tblastn : compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames
tblastx : compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
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FAST homology search All sequences .An alignment program for protein sequences created by Pearsin and Lipman in 1988.
The program is one of the many heuristic algorithms proposed to speed up sequence comparison. The basic idea is to add
a fast prescreen step to locate the highly matching segments between two sequences, and then extend these matching
segments to local alignments using more rigorous algorithms such as Smith-Waterman.
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These are fully automated sequence alignment tools for DNA and protein sequences. They return the best match over a total length of input sequences, be it a protein or a nucleic acid.
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