vecscreen(1) [debian man page]

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)

Bio::FeatureIO::vecscreen_simple(3pm)			User Contributed Perl Documentation		     Bio::FeatureIO::vecscreen_simple(3pm)

NAME

       Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3 output

SYNOPSIS

	   # read features
	   my $fin = Bio::FeatureIO->new(-file=>'vecscreen.out',
					 -format=>'vecscreen_simple');
	   my @vec_regions;
	   while (my $f = $fin->next_feature) {
	     push @vec_regions, $f;
	   }

	   # write features NOT IMPLEMENTED

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.

       This module provides parsing for vecscreen '-f 3' output, described in the vecscreen documentation as 'Text list, no alignments'

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	bioperl-l@bioperl.org		       - General discussion
	http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Robert Buels
       Email rmb32 AT cornell.edu

CONTRIBUTORS

       Based on ptt.pm by Torsten Seeman

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   _initialize
       Title   : _initialize Function: Reading? parses the header of the input
		 Writing?

   next_feature
	 Title	 : next_feature
	 Usage	 : $io->next_feature()
	 Function: read the next feature from the vecscreen output file
	 Args	 : none
	 Returns : Bio::SeqFeatureI object

   write_feature (NOT IMPLEMENTED)
	 Title	 : write_feature
	 Usage	 : $io->write_feature($feature)
	 Function: write a Bio::SeqFeatureI object in vecscreen -f 3 format
	 Example :
	 Args	 : Bio::SeqFeatureI object
	 Returns :

perl v5.14.2							    2012-03-02				     Bio::FeatureIO::vecscreen_simple(3pm)