probcons(1) [debian 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)
Check Out this Related Man Page
SIGMA(1) Manual of Sigma SIGMA(1) NAME
sigma - Simple greedy multiple alignment of non-coding DNA sequences SYNOPSIS
sigma [options] [inputfile.fasta] [inputfile2.fasta ...] Each fasta file may contain a single sequence or multiple sequences; all sequences will be aligned together. DESCRIPTION
Sigma ("Simple greedy multiple alignment") is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence. It uses a strategy of seeking the best possible gapless local alignments, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA. With real data, while "correctness" can't be directly quantified for the alignment, running the PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's alignments are superior. OPTIONS
-A --aligned_output Aligned, pretty-printed output (compare with -F option) (default: only this). See also -C. -b --bgprobfile filename Auxiliary file (in fasta format) from which to read background sequences (overridden by -B). Typically this is a file containing large quantities of similar non-coding sequence, from which background probabilities of single- and di-nucleotides may be estimated. -B --bgseqfile filename File containing background probabilities. The format is described further below. -C --caps_only Use only upper-case letters in output sequence, for compatibility with output of some other programs like ClustalW and MLagan. By default, output is mixed-case (as in Dialign), and lower-case bases are treated as not aligned. -F --fasta_output Multi-fasta output (can use both -A and -F in either order). See also -C. -n --ncorrel number Background correlation (default 2=dinucleotide; 1=single-site basecounts, 0=0.25 per base). -x, --significance number Set limit for how probable the match is by chance (default 0.002, smaller=more stringent). -h, --help Displays this list of options. MORE HELP
The "significance" parameter (-x) determines whether local alignments are accepted or rejected. The default at present is 0.002. Experiments on synthetic data (described in the paper) suggest that 0.002 is about the threshold where sigma fails to align phylogenetically-unrelated data that has moderate (yeast-like) dinucleotide correlation. Using a "background model" appropriate to the sequences being aligned greatly reduces spurious alignments on synthetic data (and, one hopes, on real data too). The simplest way to ensure this is to supply, via the -b parameter, a FASTA-format file containing large quantities of similar sequence data (eg, if one is aligning yeast sequences, supply a file containing all intergenic yeast sequence). Instead of this, if the single-site and dinucleotide frequencies are known already, they may be supplied in a file via the -B option. The file format should be: one entry per line, with the mononucleotide or dinucleotide (case-insensitive) followed by the frequency. (eg, "A 0.3", "AT 0.16", etc on successive lines.) A sample file is in the "Background" subdirectory of the source distribution (on Debian systems, this file can be found in the /usr/share/doc/sigma-align/Background directory). A file like "yeast.nc.3.freq" in the "tests" subdirectory of the MEME source distribution works fine (trinucleotide counts are ignored). REFERENCE
Please cite Sigma: Rahul Siddharthan (2006) Multiple alignment of weakly-conserved non-coding DNA sequence BMC Bioinformatics 2006, 7:143 doi:10.1186/1471-2105-7-143 Published 16 March 2006, available online at http://www.biomedcentral.com/1471-2105/7/143/ AUTHORS
Rahul Siddharthan <rsidd@imsc.res.in> Wrote sigma. If you're using Sigma for actual research, please let the author know so that he can alert you of bugfixes or new releases. Charles Plessy <charles-debian-nospam@plessy.org> Wrote the manpage in DocBook XML for the Debian distribution. COPYRIGHT
Copyright (C) 2006-2007 Rahul Siddharthan Copyright (C) 2006-2007 Charles Plessy Sigma is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. sigma 1.1 2007-04-07 SIGMA(1)