NAGRP BLAST Server Documentation

User manuals
Search utilities
  • bl2seq - given two sequences in FASTA format, find regions of local similarity
  • blastall - given sequences in FASTA format, find similar sequences in a BLAST database
  • megablast - compare highly similar nucleotide sequences
  • mpiblast - a parallel implementation of NCBI BLAST.
  • blastpgp - create protein profiles with iterative and regular expression BLAST
Sequence manipulation utilities
  • fastacmd - retrieve FASTA sequences from BLAST databases
  • formatdb - create BLAST databases from FASTA sequences
Advanced utilities
  • blastclust - automatic sequence clustering
  • rpsblast - search an RPSBLAST database using the BLAST algorithm
  • formatrpsdb - create an RPSBLAST database from sequences in Score-matrix-parameters format
  • impala - search an RPSBLAST database using the Smith-Waterman algorithm (deprecated)
  • netblast: - network-client BLAST which accesses the NCBI BLAST search engine.
Downloads
Glossary
  • profile - A position-specific scoring matrix (PSSM) created by position-specific iterated BLAST (psiblast).
  • FASTA - Originally a protein alignment algorithm, in this context FASTA refers to an uncompressed text representation of nucleotide or protein sequence data.
  • BLAST database - A set of protein or nucleotide sequences in a format suitable for efficient searching.
  • RPSBLAST database - A set of profiles in a format suitable for efficient searching.

 
The Blast Engine is a work of,
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