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