GLAM2(1) glam2 Manual GLAM2(1)NAME
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 http://bioinformatics.org.au/glam2/ 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 <plessy@debian.org>
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
PROBCONS(1) Probcons Manual PROBCONS(1)NAME
probcons - align multiple protein sequences and print to standard output
SYNOPSIS
probcons [OPTION] [MFAFILE] [MFAFILE]
DESCRIPTION
probcons is a tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and
consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date. On the BAliBASE
benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing
an average of 7% more correctly aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14%
more correctly aligned columns than those of DIALIGN.
probcons aligns sequences provided in MFA format. This format consists of multiple sequences. Each sequence in MFA format begins with a
single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than
(">") symbol in the first column.
OPTIONS -clustalw
use CLUSTALW output format instead of MFA
-c --consistency REPS
use 0 <= REPS <= 5 (default: 2) passes of consistency transformation
-ir --iterative-refinement REPS
use 0 <= REPS <=1000 (default: 100) passes of iterative-refinement
-pre --pre-training REPS
use 0 <= REPS <= 20 (default: 0) rounds of pretraining
-pairs
generate all-pairs pairwise alignments
-viterbi
use Viterbi algorithm to generate all pairs (automatically enables -pairs)
-v --verbose
Report progress while aligning (default: off)
-annot FILENAME
write annotation for multiple alignment to FILENAME
-t --train FILENAME
compute EM transition probabilities, store in FILENAME (default: no training)
-e --emissions
also reestimate emission probabilities (default: off)
-p --paramfile FILENAME
read parameters from FILENAME (default: )
-a --alignment-order
print sequences in alignment order rather than input order (default: off)
SEE ALSO
o You can find more information in the manual of ProbCons, which is located in /usr/share/doc/probcons/manual.pdf in Debian systems.
o An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, probcons-RNA(1), is also
distributed in the ProbCons Debian package.
o pc-makegnufile(1), pc-compare(1), pc-project(1), which are distributed separately in the probcons-extra package.
REFERENCE
Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence
Alignment. Genome Research 15: 330-340.
AUTHORS
Chuong Do <chuongdo@cs.stanford.edu>
Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science,
Stanford University.
Charles Plessy <charles-debian-nospam@plessy.org>
Wrote this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
This program and its manpage are in the public domain.
probcons 1.12 2007-04-04 PROBCONS(1)