Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

glam2(1) [debian man page]

GLAM2(1)							   glam2 Manual 							  GLAM2(1)

glam2 - Gapped Local Alignment of Motifs SYNOPSIS
glam2 [options] alphabet my_seqs.fa An alphabet other than p or n is interpreted as the name of an alphabet file. DESCRIPTION
GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs. OPTIONS (DEFAULT SETTINGS) -h Show all options and their default settings. -o Output file (stdout). -r Number of alignment runs (10). -n End each run after this many iterations without improvement (10000). -2 Examine both strands - forward and reverse complement. -z Minimum number of sequences in the alignment (2). -a Minimum number of aligned columns (2). -b Maximum number of aligned columns (50). -w Initial number of aligned columns (20). -d Dirichlet mixture file. -D Deletion pseudocount (0.1). -E No-deletion pseudocount (2.0). -I Insertion pseudocount (0.02). -J No-insertion pseudocount (1.0). -q Weight for generic versus sequence-set-specific residue abundances (1e+99). -t Initial temperature (1.2). -c Cooling factor per n iterations (1.44). -u Temperature lower bound (0.1). -p Print progress information at each iteration. -m Column-sampling moves per site-sampling move (1.0). -x Site sampling algorithm: 0=FAST 1=SLOW 2=FFT (0). -s Seed for pseudo-random numbers (1). SEE ALSO
glam2format(1), glam2mask(1), glam2-purge(1), glam2scan(1) The full Hypertext documentation of GLAM2 is available online at or on this computer in /usr/share/doc/glam2/. REFERENCE
If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). AUTHORS
Martin Frith Author of GLAM2. Timothy Bailey Author of GLAM2. Charles Plessy <> Formatted this manpage in DocBook XML for the Debian distribution. COPYRIGHT
The source code and the documentation of GLAM2 are released in the public domain. GLAM2 1056 05/19/2008 GLAM2(1)

Check Out this Related Man Page

hmmalign(1)							   HMMER Manual 						       hmmalign(1)

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 HMMER
Man Page