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)
Check Out this Related Man Page
FORMATDB(1) NCBI Tools User's Manual FORMATDB(1)NAME
formatdb - format protein or nucleotide databases for BLAST
SYNOPSIS
formatdb [-] [-B filename] [-F filename] [-L filename] [-T filename] [-V] [-a] [-b] [-e] [-i filename] [-l filename] [-n str] [-o] [-p F]
[-s] [-t str] [-v N]
DESCRIPTION
formatdb must be used in order to format protein or nucleotide source databases before these databases can be searched by blastall,
blastpgp or MegaBLAST. The source database may be in either FASTA or ASN.1 format. Although the FASTA format is most often used as input
to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source for other formats such as the GenBank
report. Once a source database file has been formatted by formatdb it is not needed by BLAST. Please note that if you are going to apply
periodic updates to your BLAST databases using fmerge(1), you will need to keep the source database file.
OPTIONS
A summary of options is included below.
- Print usage message
-B filename
Binary Gifile produced from the Gifile specified by -F. This option specifies the name of a binary GI list file. This option
should be used with the -F option. A text GI list may be specified with the -F option and the -B option will produce that GI list
in binary format. The binary file is smaller and BLAST does not need to convert it, so it can be read faster.
-F filename
Gifile (file containing list of gi's) for use with -B or -L
-L filename
Create an alias file named filename, limiting the sequences searched to those specified by -F.
-T filename
Set the taxonomy IDs in ASN.1 deflines according to the table in filename.
-V Verbose: check for non-unique string ids in the database
-a Input file is database in ASN.1 format (otherwise FASTA is expected)
-b ASN.1 database is binary (as opposed to ASCII text)
-e Input is a Seq-entry. A source ASN.1 database (either text ascii or binary) may contain a Bioseq-set or just one Bioseq. In the
latter case -e should be provided.
-i filename
Input file(s) for formatting
-l filename
Log file name (default = formatdb.log)
-n str Base name for BLAST files (defaults to the name of the original FASTA file)
-o Parse SeqID and create indexes. If the source database is in FASTA format, the database identifiers in the FASTA definition line
must follow the conventions of the FASTA Defline Format.
-p F Input is a nucleotide, not a protein.
-s Index only by accession, not by locus. This is especially useful for sequence sets like the EST's where the accession and locus
names are identical. Formatdb runs faster and produces smaller temporary files if this option is used. It is strongly recommended
for EST's, STS's, GSS's, and HTGS's.
-t str Title for database file [String]
-v N Break up large FASTA files into `volumes' of size N million letters (4000 by default). As part of the creation of a volume, for-
matdb writes a new type of BLAST database file, called an alias file, with the extension `nal' or `pal'.
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO blast(1), copymat(1), formatrpsdb(1), makemat(1), /usr/share/doc/blast2/formatdb.html.
NCBI 2007-10-19 FORMATDB(1)