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 <[email protected]> -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 -- View it on GitLab: https://salsa.debian.org/blends-team/med/commit/a0e78e1d4f35f6e14ab18eeceb854602263cb991 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ Blends-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit
