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>