BLAST
From Christoph's Personal Wiki
BLAST (the Basic Local Alignment Search Tool) is a service of the National Center for Biotechnology Information (NCBI). A nucleotide or protein sequence sent to the BLAST server is compared against databases at the NCBI and a summary of matches is returned to the user.
Contents
BLAST Assembled Genomes
Note: The following are examples of assembled genomes that can be used as BLAST databases. See here for complete list.
- Human
- Mouse
- Rat
- Arabidopsis thaliana
- Oryza sativa
- Bos taurus
- Danio rerio
- Drosophila melanogaster
- Gallus gallus
- Pan troglodytes
- Microbes
- Apis mellifera
Basic BLAST
- nucleotide blast
- Search a nucleotide database using a nucleotide query (Algorithms: blastn, megablast, discontiguous megablast)
- protein blast
- Search protein database using a protein query (Algorithms: blastp, psi-blast, phi-blast)
- blastx
- Search protein database using a translated nucleotide query
- tblastn
- Search translated nucleotide database using a protein query
- tblastx
- Search translated nucleotide database using a translated nucleotide query
Blast Family of Programs
The BLAST family of programs allows all combinations of DNA or protein query sequences with searches against DNA or protein databases:
- 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 the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.
- tblastn
- compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).
- tblastx
- compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.
The default matrix for all protein-protein comparisons is BLOSUM62.
Overview of database search programs
| Database | |||
|---|---|---|---|
| Protein | DNA | ||
| Query | Protein | ssearch | tfasta (translates database) |
| fasta | tfastx3 (translates database, allowing frame-shift gaps) | ||
| blastp | tblastn (translates database) | ||
| PSI-blast (simplified profile search) | |||
| DNA | fastx3 (translates query, allowing frameshift gaps) | ssearch | |
| blastx (translates query) | fasta | ||
| blastn | |||
| tblastx (translates query and database; no gaps) | |||
