debian man page for vecscreen

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)