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 © 2006-2007 Rahul Siddharthan
Copyright © 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.