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.