reprof(1) [debian man page]
REPROF(1) User Commands REPROF(1) NAME
reprof - predict protein secondary structure and solvent accessibility SYNOPSIS
reprof -i [query.blastPsiMat] [OPTIONS] reprof -i [query.fasta] [OPTIONS] reprof -i [query.blastPsiMat|query.fasta] --mutations [mutations.txt] [OPTIONS] DESCRIPTION
Predict protein secondary structure and solvent accessibility. Output Format The output format is self-explanatory, i.e. the colums of the output are described in the output file itself. OPTIONS
-i, --input=FILE Input BLAST PSSM matrix file (from Blast -Q option) or input (single) FASTA file. -o, --out=FILE Either an output file or a directory. If not provided or a directory, the suffix of the input filename (i.e. .fasta or .blastPsiMat) is replaced to create an output filename. --mutations=[all|FILE] Either the keyword "all" to predict all possible mutations or a file containing mutations one per line such as "C12M" for C is mutated to M on position 12: C30Y R31W G48D This mutation code is also attached to the output filename using "_". An additional file ending "_ORI" contains the prediction using no evolutionary information even if a BLAST PSSM matrix was provided. --modeldir=DIR Directory where the model and feature files are stored. Default: /usr/share/reprof. AUTHOR
Peter Hoenigschmid hoenigschmid@rostlab.org, Burkhard Rost EXAMPLES
Prediction from BLAST PSSM matrix for best results: reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/example.Q.reprof Prediction from FASTA file: reprof -i /usr/share/doc/reprof/examples/example.fasta -o /tmp/example.fasta.reprof Prediction from BLAST PSSM matrix file using the mutation mode: reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/mutations_example.Q.reprof --mutations /usr/share/doc/reprof/examples/mutations.txt # Result files for the above call are going to be: # /tmp/mutations_example.Q.{reprof,reprof_F172P,reprof_M1Q,reprof_N34Y,reprof_ORI} - see --mutations for a description of the extensions. COPYRIGHT
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. BUGS
https://rostlab.org/bugzilla3/enter_bug.cgi?product=reprof SEE ALSO
blast2(1) http://rostlab.org/ 1.0.1 2012-01-13 REPROF(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)