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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 data- bases. GenBank Annotation Staff use vecscreen to verify that sequences sub- mitted for inclusion in the database are free from contaminating vector se- quence. Any sequence can be screened for vector contamination using vec- screen. vecscreen searches a query for segments that match any sequence in a spe- cialized non-redundant vector database (UniVec). The search uses BLAST with parameters preset for optimal detection of vector contamination. Those seg- ments 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 se- quence may be of vector origin. Although a vecscreen search against UniVec will not identify the vector that is the most likely source of the contami- nation, this can usually be deduced from the cloning history of the se- quenced 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)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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