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)