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.TH VECSCREEN 1 2001-10-05 NCBI "NCBI Tools User's Manual"
.SH NAME
vecscreen \- find nucleic acid segments of possible vector origin
.SH SYNOPSIS
.B vecscreen
[\|\fB\-\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-f\fP\ \fIN\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
.SH DESCRIPTION
\fBvecscreen\fP is a system for quickly identifying segments of a
nucleic acid sequence that may be of vector origin. NCBI developed
\fBvecscreen\fP to minimize the incidence and impact of vector
contamination in public sequence databases. GenBank Annotation Staff
use \fBvecscreen\fP 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
\fBvecscreen\fP.
.PP
\fBvecscreen\fP 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).
.PP
\fBvecscreen\fP 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
\fBvecscreen\fP 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.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-d\fP\ \fIstr\fP
Database (default = \fBUniVec\fP)
.TP
\fB\-f\fP\ \fIN\fP
Output format:
.RS
.PD 0
.IP 0
HTML format, with alignments (default)
.IP 1
HTML format, no alignments
.IP 2
Text list, with alignments
.IP 3
Text list, no alignments
.PD
.RE
.TP
\fB\-i\fP\ \fIfilename\fP
Query File (default = \fBstdin\fP)
.TP
\fB\-o\fP\ \fIfilename\fP
VecScreen report Output File (default = \fBstdout\fP)
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
<http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen_docs.html>
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