Ubuntu Manpage: proda - multiple alignment of protein sequences with repeats and rearrangements

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.

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

COPYRIGHT

       Copyright © 2007 David Paleino

                                          april 25, 2007                                 PRODA(1)