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Alignment / Similarity Search Tools

  • BLAST
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:

 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.


  • FASTA
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.


  • ClustalW ClustalX
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.