Databases searches

• Software for searching in local databases
• Search similar sequences in databases
• Search sequences with HMM profiles in databases
• Blast post-processing

• Software for searching in local databases

GOLDEN

• golden: Fast databases entry searches by id.

• Search similar sequences in databases

FASTA

• fasta: Sequence Comparison tool.




BLAST: Basic Local Alignment Search Tool.

• blast2: NCBI-Blast2 (version 2 developped at NCBI)
• wublast2: WU-Blast2 (version 2 developped at Washington University):




PSI-BLAST

• psi-blast: Position Specific Iterative Blast




PHI-BLAST

• phi-blast: Pattern-Hit Initiated Blast

• Search sequences with HMM profiles in databases

HMMER

• hmmsearch: Search a sequence database with a profile HMM.
• hmmfetch: Retrieve an HMM from an HMM database.
• hmmpfam: Search sequences against an HMM database.

• Blast post-processing

BLAST2TAXONOMY

• blast2taxonomy: Blast Taxonomy report.




MSPCRUNCH

• mspcrunch: a filtering tool for Blast matches




MVIEW

• mview: Pretty viewer




HTML4BLAST

• html4blast: HTML blast results formatter