Bug#710324: ITP: staden -- set of DNA sequence assembly, editing and analysis tools
Hi Jonas,
considering you have files some bugs against staden-io-lib (version
1.12.x) you are most probably aware that we just have this:
$ apt-cache showsrc staden-io-lib
Package: staden-io-lib
Binary: staden-io-lib-utils, libstaden-read-dev, libstaden-read1
Version: 1.12.4-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>
Homepage: http://staden.sourceforge.net/
Priority: source
Section: science
In case there might be reasons to stick to the current 1.x series and it
makes sense to package 2.x in addition instead of simply upgrading I
would welcome if you would choose the Debian Med repository for doing so
(any DD has commit permissions) and set Debian Med team as maintainer.
Kind regards
Andreas.
On Thu, May 30, 2013 at 01:02:14AM +0200, Jonas Smedegaard wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Jonas Smedegaard <dr@jones.dk>
>
> * Package name : staden
> Version : 2.0.0b9
> Upstream Author : Medical Research Council, Laboratory of Molecular Biology
> * URL : http://staden.sourceforge.net/
> * License : unknown (need to be resolved, obviously, before releasing)
> Programming Lang: C, C++, Tcl
> Description : set of DNA sequence assembly, editing and analysis tools
>
> This is the Staden package, a collection of sequence handling and
> analysis software.
> .
> Gap4 performs sequence assembly, contig ordering based on read pair
> data, contig joining based on sequence comparisons, assembly checking,
> repeat searching, experiment suggestion, read pair analysis and contig
> editing. It has graphical views of contigs, templates, readings and
> traces which all scroll in register. Contig editor searches and
> experiment suggestion routines use confidence values to calculate the
> confidence of the consensus sequence and hence identify only places
> requiring visual trace inspection or extra data. The result is
> extremely rapid finishing and a consensus of known accuracy.
> .
> Pregap4 provides a graphical user interface to set up the processing
> required to prepare trace data for assembly or analysis, and automates
> these processes.
> .
> Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
> ZTR trace files.
> .
> Prefinish analyses partially completed sequence assemblies and suggests
> the most efficient set of experiments to help finish the project.
> .
> Tracediff and hetscan automatically locate mutations by comparing trace
> data against reference traces. They annotate the mutations found ready
> for viewing in gap4.
> .
> Spin analyses nucleotide sequences to find genes, restriction sites,
> motifs, etc. It can perform translations, find open reading frames,
> count codons, etc. Many results are presented graphically and a sliding
> sequence window is linked to the graphics cursor. Spin also compares
> pairs of sequences in many ways. It has very rapid dot matrix analysis,
> global and local alignment algorithms, plus a sliding sequence window
> linked to the graphical plots. It can compare nucleic acid against
> nucleic acid, protein against protein, and protein against nucleic
> acid.
>
>
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