formatdb(1) [debian 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)
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ASN2ALL(1) NCBI Tools User's Manual ASN2ALL(1) NAME
asn2all - generate reports from ASN.1 biological data SYNOPSIS
asn2all [-] [-A acc] [-F filename] [-G] [-J n] [-K n] [-M] [-T] [-X] [-a type] [-b] [-c] [-d path] [-f format] [-h] [-i filename] [-k] [-l] [-n policy] [-o filename] [-p path] [-r] [-v filename] [-x ext] DESCRIPTION
asn2all is primarily intended for generating reports from the binary ASN.1 Bioseq-set release files downloaded from the NCBI ftp site (ncbi-asn1 directory). It can produce GenBank and GenPept flatfiles, FASTA sequence files, INSDSet structured XML, TinySeq XML, and Sequin-style 5-column feature tables. The release files (which have the extension .aso.gz) should be uncompressed with gunzip(1), resulting in files with the extension .aso. For example, gbpri1.aso is the first file in the primate division, and the command gunzip gbpri1.aso.gz will result in gbpri1.aso being created. The original gbpri1.aso.gz file is removed after successful decompression. In asn2all, the name of the file to be processed is specified by the -i command line argument. Use -a t to indicate that it is a release file and -b to indicate that it is binary ASN.1. A text ASN.1 file obtained from Entrez can be processed by using -a a instead of -a t -b. Nucleotide and protein records can be processed simultaneously. Use the -o argument to indicate the nucleotide output file, and the -v argument for the protein output file. The -f argument determines the format to be generated, and is documented in more detail (along with other options) in the following sec- tion. OPTIONS
A summary of options is included below. - Print usage message -A accession Accession to fetch; may take the form accession,complexity,flags where complexity should normally be 0 and a flags value of -1 enables fetching of external features -F filename Accession Filter file -G Relaxed Genome Mapping -J n Seq-loc from -K n Seq-loc to -M Seq-loc Minus strand -T Use Threads -X EXtended qualifier output -a type Input ASN.1 type: a Automatic (default) c Catenated z Any e Seq-entry b Bioseq s Bioseq-set m Seq-submit t batch processing (suitable for official releases; autodetects specific type) -b Bioseq-set is Binary -c Bioseq-set is Compressed -d path Path to indexed binary ASN.1 Data -f format Output Format: g GenBank/GenPept (default) m GenBank Master Style f FASTA d CDS FASTA e Gene FASTA t Sequin-style 5-column feature table y TinySet XML (akin to FASTA) s INSDSet XML (akin to GenBank/GenPept) a structurally equivalent text ASN.1 x structurally equivalent XML c cache components -h Display extra Help message -i filename Input file name (standard input by default) -k Enable local fetching -l Lock components in advance -n policy Near FASTA policy: a All n Near only (default) f Far only -o filename Nucleotide Output file name -p path Path to files -r Enable Remote fetching -v filename Protein output file name -x ext File selection suffix when working with entire directories. (default is .aso) EXAMPLES
The command asn2all -i gbpri1.aso -a t -b -f g -o gbpri1.nuc -v gbpri1.prt will generate GenBank and GenPept reports from gbpri1.aso. AUTHOR
The National Center for Biotechnology Information. SEE ALSO
asn2asn(1), asn2ff(1), asn2fsa(1), asn2gb(1), asn2idx(1), asn2xml(1), asndhuff(1), gene2xml(1), gunzip(1). NCBI
2012-06-24 ASN2ALL(1)