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>