category: Database

programs:

• acedemo - Demonstration laboratory database
• blast2gi.py - Given output from NCBI Blast+ using the -remote option , create a file containing GI numbers of hits listed in the output
• blast_formatter - convert blast output to a differrent format
• blastdbcmd - Client for local BLAST databases
• blastdbkit.py - Install and update local BLAST databases
• blncbi - Graphical query program for NCBI databases
• blnfetch - BioLegato interface for retrieving DNA or RNA sequences from NCBI
• blpfetch - BioLegato interface for retrieving amino acid sequences from NCBI
• blsort.py - Sort a BioLegato table
• 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
• ncbiquery.py - Send an Entrez query to NCBI and return the result
• randseq - Randomize a set of sequences
• seqfetch.py - Given a set of GI (UID) or ACCESSION numbers , create a file containing the corresponding sequence entries
• 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
• 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
• xtract - converts XML into a table of data values
• xylem_identify - used by FINDKEY to extract LOCUS names from database hits
• xylem_shuffle - randomize sequences using a sliding window