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
VECSCREEN(1) NCBI Tools User's Manual VECSCREEN(1) NAME
vecscreen - find nucleic acid segments of possible vector origin SYNOPSIS
vecscreen [-] [-d str] [-f N] [-i filename] [-o filename] DESCRIPTION
vecscreen is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. NCBI developed vecscreen to minimize the incidence and impact of vector contamination in public sequence databases. GenBank Annotation Staff use vecscreen to verify that sequences submitted for inclusion in the database are free from contaminating vector sequence. Any sequence can be screened for vector contamination using vecscreen. vecscreen searches a query for segments that match any sequence in a specialized non-redundant vector database (UniVec). The search uses BLAST with parameters preset for optimal detection of vector contamination. Those segments of the query that match vector sequences are categorized according to the strength of the match, and their locations are displayed (see example positive result). vecscreen is designed to quickly check a nucleic acid sequence for the presence of vector contamination and to show which segments within the sequence may be of vector origin. Although a vecscreen search against UniVec will not identify the vector that is the most likely source of the contamination, this can usually be deduced from the cloning history of the sequenced DNA. OPTIONS
A summary of options is included below. - Print usage message -d str Database (default = UniVec) -f N Output format: 0 HTML format, with alignments (default) 1 HTML format, no alignments 2 Text list, with alignments 3 Text list, no alignments -i filename Query File (default = stdin) -o filename VecScreen report Output File (default = stdout) AUTHOR
The National Center for Biotechnology Information. SEE ALSO
<http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen_docs.html> NCBI
2001-10-05 VECSCREEN(1)