hmmalign(1) [debian man page]
hmmalign(1) HMMER Manual hmmalign(1) NAME
hmmalign - align sequences to a profile HMM SYNOPSIS
hmmalign [options] <hmmfile> <seqfile> DESCRIPTION
Perform a multiple sequence alignment of all the sequences in seqfile, by aligning them individually to the profile HMM in hmmfile. The new alignment is output to stdout in Stockholm format. The sequences in seqfile are aligned in unihit local alignment mode. Therefore they should already be known to contain a single domain; they should not contain more than one domain. They may be fragments. The optimal alignment may assign some residues as nonhomologous (N and C states), in which case these residues are still included in the resulting alignment, but shoved to the outer edges. To trim these nonhomologous residues from the result, see the --trim option. OPTIONS
-h Help; print a brief reminder of command line usage and all available options. -o <f> Direct the output alignment to file <f>, rather than to stdout. --allcol Include columns in the output alignment for every match (consensus) state in the hmmfile, even if it means having all-gap columns. This is useful in analysis pipelines that need to be able to maintain a predetermined profile HMM architecture (with an unchanging number of consensus columns) through an hmmalign step. --mapali <f> Merge the existing alignment in file <f> into the result, where <f> is exactly the same alignment that was used to build the model in hmmfile. This is done using a map of alignment columns to consensus profile positions that is stored in the hmmfile. The multi- ple alignment in <f> will be exactly reproduced in its consensus columns (as defined by the profile), but the displayed alignment in insert columns may be altered, because insertions relative to a profile are considered by convention to be unaligned data. --trim Trim nonhomologous residues (assigned to N and C states in the optimal alignments) from the resulting multiple alignment output. --amino Specify that all sequences in seqfile are proteins. By default, alphabet type is autodetected from looking at the residue composi- tion. --dna Specify that all sequences in seqfile are DNAs. --rna Specify that all sequences in seqfile are RNAs. --informat <s> Declare that the input seqfile is in format <s>. Accepted sequence file formats include FASTA, EMBL, Genbank, DDBJ, Uniprot, Stock- holm, and SELEX. Default is to autodetect the format of the file. --outformat <s> Specify that the msafile is in format <s>. Currently the accepted multiple alignment sequence file formats only include Stockholm and SELEX. Default is to autodetect the format of the file. SEE ALSO
See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package. For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@). COPYRIGHT
@HMMER_COPYRIGHT@ @HMMER_LICENSE@ For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@). AUTHOR
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmalign(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)