fastacmd(1) [debian man page]
FASTACMD(1) NCBI Tools User's Manual FASTACMD(1) NAME
fastacmd - retrieve FASTA sequences from a BLAST database SYNOPSIS
fastacmd [-] [-D N] [-I] [-L start,stop] [-P N] [-S N] [-T] [-a] [-c] [-d str] [-i str] [-l N] [-o filename] [-p type] [-s str] [-t] DESCRIPTION
fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the `-o' option. An example fastacmd call would be fastacmd -d nr -s p38398 OPTIONS
A summary of options is included below. - Print usage message -D N Dump the entire database in some format: 1 fasta 2 GI list 3 Accession.version list -I Print database information only (overrides all other options) -L start,stop Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence) -P N Retrieve sequences with Protein Identification Group (PIG) N. -S N Strand on subsequence (nucleotide only): 1 top (default) 2 bottom -T Print taxonomic information for requested sequence(s) -a Retrieve duplicate accessions -c Use ^A ( 01) as non-redundant defline separator -d str Database (default is nr) -i str Input file with GIs/accessions/loci for batch retrieval -l N Line length for sequence (default = 80) -o filename Output file (default = stdout) -p type Type of file: G guess (default): look for protein, then nucleotide T protein F nucleotide -s str Comma-delimited search string(s). GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag' -t Definition line should contain target GI only EXIT STATUS
0 Completed successfully. 1 An error (other than those below) occurred. 2 The BLAST database was not found. 3 A search (accession, GI, or taxonomy info) failed. 4 No taxonomy database was found. AUTHOR
The National Center for Biotechnology Information. SEE ALSO
blast(1), /usr/share/doc/blast2/fastacmd.html. NCBI
2005-11-04 FASTACMD(1)
Check Out this Related Man Page
BLASTCLUST(1) NCBI Tools User's Manual BLASTCLUST(1) NAME
blastclust - BLAST score-based single-linkage clustering SYNOPSIS
blastclust [-] [-C] [-L X] [-S X] [-W N] [-a N] [-b F] [-c filename] [-d filename] [-e F] [-i filename] [-l filename] [-o filename] [-p F] [-r filename] [-s filename] [-v [filename]] DESCRIPTION
blastclust automatically and systematically clusters protein or DNA sequences based on pairwise matches found using the BLAST algorithm in case of proteins or Mega BLAST algorithm for DNA. In the latter case a single Mega BLAST search is performed for all the sequences combined against a database created from the same sequences. blastclust finds pairs of sequences that have statistically significant matches and clusters them using single-linkage clustering. OPTIONS
A summary of options is included below. - Print usage message -C Complete unfinished clustering -L X Length coverage threshold (default = 0.9) -S X Score coverage threshold (bit score / length if < 3.0, percentage of identities otherwise; default = 1.75) -W N Use words of size N (length of best perfect match; zero invokes default behavior: 3 for proteins, 32 for nucleotides) -a N Number of CPU's to use (default = 1) -b F Do not require coverage on both neighbours -c filename Read advanced options from configuration file filename -d filename Input as a database -e F Disable id parsing in database formatting -i filename FASTA input file (program will format the database and remove files in the end; default = stdin) -l filename Restrict reclustering to id list in filename -o filename Output file for list of clusters (default = stdout) -p F Input is nucleotides, not proteins. -r filename Restore neighbors for reclustering from filename -s filename Save all neighbours to filename -v [filename] Print verbose progress messages (to filename) AUTHOR
The National Center for Biotechnology Information. SEE ALSO
blast(1), formatdb(1), /usr/share/doc/blast2/blastclust.html, <http://www.ncbi.nlm.nih.gov/BLAST/> NCBI
2004-06-25 BLASTCLUST(1)