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>