proda - Online in the Cloud

PROGRAM:

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:

· the MFA format consists of multiple sequences;

· each sequence in the 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.

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:

· the ClustalW format consists of a single header line followed by sequence data in
blocks of 50 alignment positions;

· each block consists of:

· one line of data for each of the sequences in the alignment - in particular, the
name of the sequence;

· 50 characters of the alignment;

· one annotation line indicating fully conserved (*), strongly-conserved (:), or
weakly-conserved columns (.);

· 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:

· the FASTA format consists of all the sequences given in the input files;

· each sequence in the FASTA 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;

· 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.

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