AMAP(1)
NAME
amap - Protein multiple alignment by sequence annealing
SYNOPSIS
amap [OPTION] [MFAFILE] [MFAFILE]
DESCRIPTION
AMAP is a tool to perform multiple alignment of peptidic sequences. It
utilizes posterior decoding, and a sequence-annealing alignment,
instead of the traditional progressive alignment method. It is the only
alignment program that allows to control the sensitivity / specificity
tradeoff. It is based on the ProbCons source code, but uses alignment
metric accuracy and eliminates the consistency transformation.
In its default configuration, AMAP is tuned to maximize the expected
Alignment Metric Accuracy (AMA) score - a new alignment accuracy
measure, based on a metric for the multiple-alignment space, which
integrates sensitivity and specificity into a single balanced measure.
AMA is defined as the fraction of correctly aligned residues (either to
another residue or to a gap) out of the total number of residues in all
the sequences.
amap 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: 0) passes of consistency
transformation - -ir --iterative-refinement REPS
- use 0 <= REPS <=1000 (default: 0) 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) - -g --gap-factor GF
- use GF as the gap-factor parameter, set to 0 for best sensitivity, higher values for better specificity (default: 0.5)
- -w --edge-weight-threshold W
- stop the sequence annealing process when best edge has lower weight
than W, set to 0 for best sensitivity, higher values for better
specificity (default: 0) - -prog --progressive
- use progressive alignment instead of sequence annealing alignment
(default: off) - -noreorder --no-edge-reordering
- disable reordering of edges during sequence annealing alignment
(default: off) - -maxstep --use-max-stepsize
- use maximum improvement step size instead of tGf edge ranking
(default: off) - -print --print-posteriors
- only print the posterior probability matrices (default: off)
- -gui START STEP
- print output for the AMAP Display Java based GUI (default: )
starting at weight START (default: infinity) with step size STEP (default: )
EXAMPLES
To run AMAP with the default options change to the align directory and
type:
% amap <multi-fasta-file-name>
If no file name is provided the list of options are printed.
In order to use the AMAP Display run AMAP with the -gui option, and
save the output to a file, then use the file as the input to
AmapDisplay. For example, type:
% align/amap -gui examples/BB12020.tfa > examples/BB12020.tfa.out
% java -jar display/AmapDisplay.jar examples/BB12020.tfa.out
(on Debian systems, the examples directory is in
/usr/share/doc/amap-align/examples
NOTE
In older versions ( < 2.0-1) of the package for Debian(TM) systems, the
amap command was renamed amap-align because there was already another
tool called amap (which performs some computer network diagnostics). A
symbolic link amap-align is still provided for upgrade purposes but
will be removed in Debian releases posterior to Etch (Debian 4.0).
SEE ALSO
The current version of AMAP uses the PROBCONS 1.09 code base for some
of the input/output procedures, and for the calculation of posterior
probabilities (see PROBCONS.README in /usr/share/doc/amap-align/).
Future releases might implement the algorithm using a new independent
code base.
On Debian(TM) systems, probcons(1) is available in the probcons
package.
REFERENCES
For more details on AMAP and AMA, see Schwartz, Ariel S., Myers, Eugene
W., and Pachter, Lior. Alignment Metric Accuracy (Submitted for
publication). For more details on sequence-annealing, see Schwartz,
Ariel S. and Pachter, Lior. Multiple Alignment by Sequence Annealing
(Submitted for publication).
PROBCONS was published in 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
- Ariel Schwartz <sariel@cs.berkeley.edu>
- Upstream author of AMAP
- Chuong Do
- Wrote Probcons, on which AMAP is based.
- Charles Plessy> <charles-debian-nospam@plessy.org>
- Wrote this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
- AMAP, PROBCONS, and this manual page have been made freely available as
PUBLIC DOMAIN software and hence are not subject to copyright in the
United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions. AMAP, PROBCONS
and this manual page are distributed WITHOUT WARRANTY, express or
implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
loss due to reliance on the program.