Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/FBB/year_04/doc/BLAST_help/ Дата изменения: Thu Oct 21 20:03:36 2004 Дата индексирования: Tue Oct 2 12:54:34 2012 Кодировка:

Downloads

• Standalone utilities
• BLAST databases
• RPSBLAST databases

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
•     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
•     makemat / copymat - convert a set of profiles into an RPSBLAST database
•     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)

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.