MAKEMAT(1) NCBI Tools User's Manual MAKEMAT(1)NAME
makemat - convert binary profiles into portable ASCII form
SYNOPSIS
makemat [-] [-E N] [-G N] [-H] [-P filename] [-S X] [-U str] [-d str] [-z N]
DESCRIPTION
makemat converts a collection of binary profiles, created by the -C option of PSI-BLAST, into portable ASCII form.
OPTIONS
A summary of options is included below.
- Print usage message
-E N Cost to extend a gap (default = 1)
-G N Cost to open a gap (default = 11)
-H Print help; overrides all other arguments
-P filename
Database name for profile database (default = stdin)
-S X Scaling factor for matrix outputs to avoid round-off problems (default = 100)
-U str Underlying Matrix (default = BLOSUM62)
-d str Underlying sequence database used to make profiles (default = nr)
-z N Effective length of the profile database (0 for length of -d option)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO blast(1), copymat(1), /usr/share/doc/blast2/impala.html
NCBI 2004-06-25 MAKEMAT(1)
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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)