[Blends-commit] [Git][blends-team/med][master] Update bio - uploaded ESTScan to new

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Blends Team / med


Commits:
a0e78e1d by Steffen Möller at 2018-05-31T22:57:19+00:00
Update bio - uploaded ESTScan to new
- - - - -


1 changed file:

- tasks/bio


Changes:

=====================================
tasks/bio
=====================================
--- a/tasks/bio
+++ b/tasks/bio
@@ -2067,39 +2067,6 @@ Pkg-Description: processes, clusters and annotates EST data
  a MySQL database or web-browsable search tool.
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 
-Recommends: estscan
-Homepage: http://estscan.sourceforge.net/
-License: free
-Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: detect coding regions in DNA sequences, even if of low quality
- ESTScan is a program that can detect coding regions in DNA sequences,
- even if they are of low quality. It will also detect and correct
- sequencing errors that lead to fr ameshifts.
- .
- ESTScan is not a gene prediction program, nor is it an open reading
- frame detector. In fact, its strength lies in the fact that it does
- not require an open reading frame to detect a coding region. As a
- result, the program may miss a few translated amino acids at either
- the N or the C terminus, but will detect coding regions with high
- selectivity and sensitivity.
- .
- Similarly to GENSCAN, ESTScan uses a Markov model to represent the
- bias in hexanucleotide usage found in coding regions relative to
- non-coding regions. Additionally, ESTScan allows insertions and
- deletions when these improve the coding region statistics. Further
- details can be found at:
- http://www.ch.embnet.org/software/ESTScan2_help.html
- .
- References:
-  * Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003) Modeling sequencing
-    errors by combining Hidden Markov models Bioinformatics 19,
-    ii103-ii112.
-  * Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for
-    detecting, evaluating, and reconstructing potential coding regions in
-    EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48.
-Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-
 Recommends: lamarc
 Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
@@ -2412,6 +2379,9 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 
 Recommends: trace2dbest
 
+Recommends: estscan
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
 Recommends: profit
 WNPP: 525428
 Remark: The authors need to change the license, still.



View it on GitLab: https://salsa.debian.org/blends-team/med/commit/a0e78e1d4f35f6e14ab18eeceb854602263cb991

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