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VECSCREEN(1)		   NCBI	Tools User's Manual		  VECSCREEN(1)

       vecscreen - find	nucleic	acid segments of possible vector origin

       vecscreen [-] [-d str] [-f N] [-i filename] [-o filename]

       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 se-
       quence databases. GenBank Annotation Staff use vecscreen	to verify that
       sequences submitted for inclusion in the	database are free from contam-
       inating vector sequence.	Any sequence can be screened for  vector  con-
       tamination 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 contamina-
       tion. Those segments of the query that match vector sequences are cate-
       gorized 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.

       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)

       The National Center for Biotechnology Information.


NCBI				  2001-10-05			  VECSCREEN(1)


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