This is the command vecscreen that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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)
Use vecscreen online using onworks.net services
