category: Sequence - Database Similarity Search

programs:

• blastn - search DNA database using DNA query
• blastp - search protein database using protein query
• BlastViewer - view and analyze BLAST output
• blastx - search protein database using auto-translated DNA query
• 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
• map_db - read a FASTA (0), GENBANK flat file (1) PIR/VMS (5) or GCG binary (6) sequence database and produce the offsets necessary for efficient memory mapping
• relate - Statistical significance of database similarity
• ssearch - Rigorous Smith-Waterman database similarity search
• tblastn - search auto-translated DNA database using protein query
• tblastx - search auto-translated DNA database using auto-translated DNA query
• 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