[Cdd-commits] r1066 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Mon Sep  8 12:29:08 2008
New Revision: 1066

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added estferret


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Sep  8 12:29:08 2008
@@ -2205,3 +2205,52 @@
  .
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
+
+Depends: estferret
+Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
+License: to be clarified
+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: processes, clusters and annotates EST data
+ ESTFerret processes, clusters and annotates EST data. It is
+ user-configurable. Results are currently stored in a series of text
+ tables. Annotation consists of searches against use r-defined blast
+ databases, prosite, GO and allocation of EC numbers where possible.
+ .
+ EST-ferret is a user-configurable, automated pipeline for the
+ convenient analysis of EST sequence data that includes all of the
+ necessary steps for cleanup and trimming, submission to external
+ sequence repositories, clustering, identification by BLAST homology
+ searches and by searches of protein domain databases, annotation with
+ computer-addressable terms and production of outputs for direct entry
+ into microarray analysis packages. It is composed of several widely
+ used, open-source algorithms, including PHRED, CAP3, BLAST, and a
+ range of sequence and annotation databases, including Gene Ontology
+ and Conserved Domain Database to deliver a putative identity and a
+ detailed annotation of each clone. It can be run either step-by-step
+ to track the outputs, or as a single batch process. Users can easily
+ edit the configuration file to define parameter settings.
+ .
+ This package has five major components: (1) ESTs coding system; (2)
+ sequence processing; (3) sequence clustering; (4) sequence annotating
+ and (5) storage and reporting of results. DNA trace files are renamed
+ and converted into FASTA format, cleaned and submitted to
+ dbEST(Boguski, et al, 1993). Sequence assembly uses two rounds of
+ CAP3 to assemble the ESTs into groups corresponding to separate gene
+ families and unique genes. Sequence identification and annotation is
+ provided by a series of BLAST homology searches (Parallel_BLAST and
+ Priority_BLAST) against user-defined sequence databases implemented
+ with the NCBI BLASTALL algorithm. The BLAST results are parsed and
+ annotation terms that reflect functional attributes are captured from
+ Gene Ontology (The Gene Ontology Consortium, 2000), KEGG and Enzyme
+ Commission (EC) databases and applied to each of the clones. CDD (and
+ InterPro) searches are performed for seeking protein domains in the
+ sequences. Other options are provided to run PatSearch, RepeatMasker
+ and BLAT to find UTRs, repeats and EST candidates in
+ genomes. Finally, the package generates analysis reports in a variety
+ of flat file formats, sources of which can be serve as inputs for
+ some gene annotation and gene expression profiling tools, and also as
+ a MySQL database or web-browsable search tool.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html