PRODA(1)

NAME

proda - multiple alignment of protein sequences with repeats and
rearrangements

SYNOPSIS

proda [option] [mfafile] [> output]

DESCRIPTION

This manual page documents briefly the proda command.

proda (Protein Domain Aligner) is public domain software for generating multiple alignments of protein sequences with repeats and
rearrangements, e.g. proteins with multiple domains.

Given a set of protein sequences as input, ProDA first finds local
pairwise alignments between all pairs of sequences, then forms blocks
of alignable sequence fragments, and finally generates multiple
alignments of the blocks. ProDA relies on many techniques used in
probcons (<http://probcons.stanford.edu>), a recent multiple aligner that shows high accuracy in a number of popular benchmarks.

INPUT FORMAT

Proda accepts input files in the MFA format. The MFA format is
specified below:

o the MFA format consists of multiple sequences;

o each sequence in the MFA format begins with a single-line: description, followed by lines of sequence data;
o the description line is distinguished from the sequence data by a: greater-than (">") symbol in the first column.

OUTPUT FORMAT

For a set of input sequences, Proda usually outputs several blocks in
turn, each consists of alignable sequence fragments. Each block is
followed by its multiple alignment.

A block is specified by listing its sequence fragments. Each fragment
is output as sequence_name(start-end), where sequence_name is the name of the original sequence and start and end are positions at which the
fragment begins and ends respectively.

Proda produces block alignments in the ClustalW (ALN) format described below:

o the ClustalW format consists of a single header line followed by: sequence data in blocks of 50 alignment positions;
o each block consists of:: o one line of data for each of the sequences in the alignment
in particular, the name of the sequence;; o 50 characters of the alignment;; o one annotation line indicating fully conserved (*),
strongly-conserved (:), or weakly-conserved columns (.);
o the description line is distinguished from the sequence data by a: greater-than (">") symbol in the first column.
FASTA format for output: If the -fasta option is specified, then, in addition to regular output, ProDA produces a file containing block alignments in the FASTA format. The output file has the same name as the first input file and extension ".fasta". Two consecutive block alignments are separated by a line
containing character '#'.; The FASTA format is described below:; o the FASTA format consists of all the sequences given in the input
files;; o each sequence in the FASTA format begins with a single-line
description, followed by lines of sequence data;; o the description line is distinguished from the sequence data by a
greater-than (">") symbol in the first column;; o aligned residues are in upper case, unaligned residues are in lower
case.; Since a final alignment contains each sequence only once, this option
should be used only if input sequences do not contain repeats.

OPTIONS

-L [min_length]: Set minimal alignment length equal to [min_length].; ProDA finds alignments of length greater than or equal to a
threshold L. By default, L = 30. This option sets the threshold to [min_length].
-posterior: Use posterior decoding when computing local pairwise
alignments.; ProDA computes local pairwise alignments between two sequences using a pair-HMM and either Viterbi decoding or posterior
decoding. The default option is using Viterbi decoding which is faster than posterior decoding but may be less accurate.
Turning on this option instructs the aligner to use posterior
decoding instead. In the example above, the output was
generated with -posterior option turned on.
-silent: Do not report progress while aligning.; Turning on this option instructs the aligner not to report the progress while aligning. By default, ProDA reports the progress on all pairwise alignments, block generation, and on block
alignment. Since some stages of the algorithm, especially
pairwise alignment, may take long time, reporting progress
makes the program look alive while running.
-tran: Use transitivity when forming blocks of alignable sequence
fragments.; Two sequence fragments are directly alignable if they are parts of a local pairwise alignment. By default, two fragments are
considered alignable if and only if they are directly
alignable. Turning on this option instructs the aligner to
consider two fragments alignable when they are directly
alignable or when both of them are directly alignable to a
third fragment.
-fasta: Use FASTA output format in addition to the ClustalW format.; When this option is turned on, the aligner generates output in the FASTA format and stores in a file with the same name as the first input file and extension ".fasta", in addition to the
normal output to stdout. This option should be used only if
input sequences do not contain repeats.

AUTHOR

This manual page was written by David Paleino <d.paleino@gmail.com> for the Debian(TM) system (but may be used by others). This man page is
released under the same conditions as the software, that is Public
Domain.

This software has been released in Public Domain by Phuong T.M., Do
C.B., Edgar R.C. and Batzoglou S. in "Multiple alignment of protein
sequences with repeats and rearrangements", Nucleic Acids Research 2006 - 34(20), 5932-5942

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