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-   -   Bug#611828: ITP: probalign -- multiple sequence alignment using partition function posterior probabilities (http://www.linux-archive.org/debian-development/484310-bug-611828-itp-probalign-multiple-sequence-alignment-using-partition-function-posterior-probabilities.html)

02-02-2011 03:39 PM

Bug#611828: ITP: probalign -- multiple sequence alignment using partition function posterior probabilities
 
Package: wnpp
Severity: wishlist
Owner: andreas@an3as.eu

* Package name : probalign
Version : 1.4
Upstream Author : Usman Roshan <usman@cs.njit.edu>
* URL : http://cs.njit.edu/usman/probalign/
* License : Public Domain
Programming Lang: C++
Description : multiple sequence alignment using partition function posterior probabilities
Probalign uses partition function posterior probability estimates to
compute maximum expected accuracy multiple sequence alignments. It
performs statistically significantly better than the leading alignment
programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0,
HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on
datasets containing N/C terminal extensions and on datasets with long
and heterogeneous length sequences. On heteregeneous length datasets
containing repeats Probalign alignment accuracy is 10% and 15% than the
other three methods when standard deviation of length is at least 300
and 400.

The package will be maintained by the Debian Med packaging team and
is ready for upload at
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/probalign/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/probalign/trunk/


-- System Information:
Debian Release: squeeze/sid
APT prefers stable
APT policy: (500, 'stable')
Architecture: i386 (i686)



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Tanguy Ortolo 02-04-2011 08:33 AM

Bug#611828: ITP: probalign -- multiple sequence alignment using partition function posterior probabilities
 
Hello.

Le mercredi 02 février 2011, andreas@an3as.eu a écrit :
> Description : multiple sequence alignment using partition function posterior probabilities

Is that about DNA sequences? I think this should be explicited in the
description, with something like:
detect multiple sequence alignment in DNA sequences

(This is just an example, as I do not know this domain this description
may be completely wrong)

--
,--.
: /` ) Tanguy Ortolo <xmpp:tanguy@ortolo.eu> <irc://irc.oftc.net/Elessar>
| `-' Debian Maintainer
\_

Charles Plessy 02-05-2011 05:27 AM

Bug#611828: ITP: probalign -- multiple sequence alignment using partition function posterior probabilities
 
Le Fri, Feb 04, 2011 at 10:33:05AM +0100, Tanguy Ortolo a écrit :
>
> Le mercredi 02 février 2011, andreas@an3as.eu a écrit :
> > Description : multiple sequence alignment using partition function posterior probabilities
>
> Is that about DNA sequences? I think this should be explicited in the
> description, with something like:
> detect multiple sequence alignment in DNA sequences

Dear Tanguy,

probalign can align DNA and protein sequences. It is a frequent request on this
list to add more information in the synopsis so that readers can know what kind
of sequence is aligned, without any other information like the long
description, Debtags or the package's section. But we only have 80 characters
to for the synopsis…

Here are synopsis for other multiple sequence alignment programs:

boxshade - Pretty-printing of multiple sequence alignments
dialign-tx - Segment-based multiple sequence alignment
dialign - Segment-based multiple sequence alignment
kalign - Global and progressive multiple sequence alignment
mafft - Multiple alignment program for amino acid or nucleotide sequences
mummer - Efficient sequence alignment of full genomes
muscle - Multiple alignment program of protein sequences
poa - Partial Order Alignment for multiple sequence alignment
probcons - PROBabilistic CONSistency-based multiple sequence alignment
proda - multiple alignment of protein sequences
sigma-align - Simple greedy multiple alignment of non-coding DNA sequences

In general, we try to reproduce the upstream short description. This is the
case for probalign.

Unless this is causing significant confusion, like mislead users from other
fields wasting their time installing bioinformatics package, I would recommend
to keep the short description as it is.

Have a nice week-end,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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