sindex(1) [debian man page]
sindex(1) Biosquid Manual sindex(1) NAME
sindex - index a sequence database for sfetch SYNOPSIS
sindex [options] seqfile1 [seqfile2...] DESCRIPTION
sindex indexes one or more seqfiles for future sequence retrievals by sfetch. An SSI ("squid sequence index") file is created in the same directory with the sequence files. By default, this file is called <seqfile>.ssi. If there is more than one sequence file on the command line, the SSI filename will be constructed from the last sequence file name. This may not be what you want; see the -o option to specify your own name for the SSI file. sindex is capable of indexing large files (>2 GB) if optional LFS support has been enabled at compile-time. See INSTALL instructions that came with @PACKAGE@. OPTIONS
-h Print brief help; includes version number and summary of all options, including expert options. -o <ssi outfile> Direct the SSI index to a file named <outfile>. By default, the SSI file would go to <seqfile>.ssi. EXPERT OPTIONS
--64 Force the SSI file into 64-bit (large seqfile) mode, even if the seqfile is small. You don't want to do this unless you're debug- ging. --external Force sindex to do its record sorting by external (on-disk) sorting. This is only useful for debugging, too. --informat <s> Specify that the sequence file is definitely in format <s>; blocks sequence file format autodetection. This is useful in automated pipelines, because it improves robustness (autodetection can occasionally go wrong on a perversely misformed file). Common examples include genbank, embl, gcg, pir, stockholm, clustal, msf, or phylip; see the printed documentation for a complete list of accepted format names. --pfamseq A hack for Pfam; indexes a FASTA file that is known to have identifier lines in format ">[name] [accession] [optional description]". Normally only the sequence name would be indexed as a primary key in a FASTA SSI file, but this allows indexing both the name (as a primary key) and accession (as a secondary key). SEE ALSO
afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sreformat(1), strans- late(1), weight(1). AUTHOR
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me. Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu Biosquid 1.9g January 2003 sindex(1)
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cmemit(1) Infernal Manual cmemit(1) NAME
cmemit - generate sequences from a covariance model SYNOPSIS
cmemit [options] cmfile seqfile DESCRIPTION
cmemit reads the covariance model(s) (CMs) in cmfile and generates a number of sequences from the CM(s); or if the -c option is selected, generates a single majority-rule consensus. This can be useful for various application in which one needs a simulation of sequences consis- tent with a sequence family consensus. By default, cmemit generates 10 sequences and outputs them in FASTA (unaligned) format to seqfile. GENERAL OPTIONS
-h Print brief help; includes version number and summary of all options, including expert options. -o <f> Save the synthetic sequences to file <f> rather than writing them to stdout. -n <n> Generate <n> sequences. Default is 10. -u Write the generated sequences in unaligned format (FASTA). This is the default, so this option is probably useless. -a Write the generated sequences in an aligned format (STOCKHOLM) with consensus structure annotation rather than FASTA. -c Predict a single majority-rule consensus sequence instead of sampling sequences from the CM's probability distribution. Highly con- served residues (base paired residues that score higher than 3.0 bits, or single stranded residues that score higher than 1.0 bits) are shown in upper case; others are shown in lower case. -l Configure the CMs into local mode before emitting sequences. See the User's Guide for more information on locally configured CMs. -s <n> Set the random seed to <n>, where <n> is a positive integer. The default is to use time() to generate a different seed for each run, which means that two different runs of cmemit on the same CM will give different results. You can use this option to generate repro- ducible results. --devhelp Print help, as with -h , but also include undocumented developer options. These options are not listed below, are under development or experimental, and are not guaranteed to even work correctly. Use developer options at your own risk. The only resources for understanding what they actually do are the brief one-line description printed when --devhelp is enabled, and the source code. EXPERT OPTIONS
--rna Specify that the emitted sequences be output as RNA sequences. This is true by default. --dna Specify that the emitted sequences be output as DNA sequences. By default, the output alphabet is RNA. --tfile <f> Dump tabular sequence parsetrees (tracebacks) for each emitted sequence to file <f>. Primarily useful for debugging. --exp <x> Exponentiate the emission and transition probabilities of the CM by <x> and then renormalize those distributions before emitting sequences. This option changes the CM probability distribution of parsetrees relative to default. With <x> less than 1.0 the emitted sequences will tend to have lower bit scores upon alignment to the CM with cmalign. With <x> greater than 1.0, the emitted sequences will tend to have higher bit scores upon alignment to the CM. This bit score difference will increase as <x> moves further away from 1.0 in either direction. If <x> equals 1.0, this option has no effect relative to default. This option is useful for generating sequences that are either difficult ( <x> < 1.0) or easy ( <x> > 1.0) for the CM to distinguish as homologous from back- ground, random sequence. --begin <n> Truncate the resulting alignment by removing all residues before consensus column <n>, where <n> is a positive integer no greater than the consensus length of the CM. Must be used in combination with --end and either -a or --shmm (a developer option). --end <n> Truncate the resulting alignment by removing all residues after consensus column <n>, where <n> is a positive integer no greater than the consensus length of the CM. Must be used in combination with --begin and either -a or --shmm (a developer option). SEE ALSO
For complete documentation, see the User's Guide (Userguide.pdf) that came with the distribution; or see the Infernal web page, http://infernal.janelia.org/. COPYRIGHT
Copyright (C) 2009 HHMI Janelia Farm Research Campus. Freely distributed under the GNU General Public License (GPLv3). See the file COPYING that came with the source for details on redistribution conditions. AUTHOR
Eric Nawrocki, Diana Kolbe, and Sean Eddy HHMI Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 http://selab.janelia.org/ Infernal 1.0.2 October 2009 cmemit(1)