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readseq for DEBIAN
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This version is built against the NCBI libraries but it seems
quite buggy: please report any problem with ASN/1 conversions
<http://bugs.debian.org/>.
I need this package to build Arb (http://www.arb-home.de).
There was a bug report (#43372) about a new version (version 2).
I decided to use the latest sources of version 1 which are in C
because I need exactly this C version. I will not package version 2
for the following reasons:
- Java adds en extra dependency of java-virtual-machine which
would bother my users and me
- most certainly it would let readseq go to contrib which I want
to avoid (not checked)
- I really need the C version for Arb.
If somebody really wants to have readseq Version 2 packaged (which
might make sense for sure) this should be made as separate package
readseq2. In this case please double check, whether it can go into
main.
The new version can be found at
ftp://ftp.bio.indiana.edu/molbio/readseq/version2
Quote from the documentation of version 2:
This release version 2, first available in 1999, continues support for
the "classic" C version, in that it supports the same command-line
options, but has extensions for sequence documentation, feature table
and other additions, plus new sequence format conversions, and a lot
of bug fixing. This java version is also more efficient, working
faster than the compiled C classic version. It still isn't efficient
enough to handle large sequences (genome sized or full GenBank/EMBL
data release files).
Andreas Tille <tille@debian.org> Thu, 25 Oct 2001 09:42:26 +0200
Starting with readseq 1-4, support for two more sequence formats was added:
LinAll format: used by the 'LinAll' and 'ConStruct' RNA structure packages
from the Duesseldorf biophysics group.
Vienna RNA format: used by the Vienna RNA package available from the
Theoretical Chemistry group at Vienna University.
Michael Schmitz <schmitz@debian.org> Wed, 11 Dec 2002 13:38:05 +0200
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