Category: Database
Programs:
acedemo - Demonstration laboratory database
blastcl3 - run BLAST remotely at NCBI
dbstat - Calculates amino acid frequencies for one or more proteins
dGDE - GDE interface for leash
fasta - Sequence database similarity
fastf - compare mixed peptides to a protein database
fastm - compare ordered peptides (or short DNA sequences) to a protein or DNA database
fasts - compare unordered peptides to a protein database
fastx - Database similarity - allow frameshifts between codons
fasty - Database similarity - Allow frameshifts within codons
features - extract features from GenBank flatfile entries
fetch - retrieve entries from local flatfile database by name or accession number
findkey - Keyword search on local flatfile database
getloc - retrieve entries from a local flatfile database
getob - Parse features from GenBank flatfiles
leash - command line interface for SeqHound API
nclever - Network command-line Entrez
randseq - Randomize a set of sequences
shuffle - randomize sequences using a sliding window
splitdb - split a GenBank flatfile into a database containing annotation, sequence and index
ssearch - Rigorous Smith-Waterman database similarity search
tace - text interface to ACeDB
taverna - Graphic workflow designer
tfasta - Database similarity with translated DNA database
tfastf - compare mixed peptides to a translated DNA database
tfasts - compare unordered peptides to a translated DNA database
tfastx - compare a protein to a DNA database, calculating similarities with frameshifts
tfasty - compare a protein to a DNA database, calculating similarities with frameshifts
xace - Graphic interface to ACeDB
xylem_identify - used by FINDKEY to extract LOCUS names from database hits