[Transdecoder-users] Announcement: TransDecoder v2.0

[Brian H. <bh...@br...>]

Greetings all.

A new and revised version of TransDecoder is now available.  Note, we've
moved the project to github, so please visit the new website:

  http://transdecoder.github.io

and we have a new google group for user support and discussions at:

  https://groups.google.com/forum/#!forum/transdecoder-users


This new version of TransDecoder has the following features:

Blast homology (new) in addition to Pfam domain hits (earlier) can be used
to ensure that protein-homologous regions are retained among the coding
region predictions.

The software now runs in two (or 3) distinct phases:

1.  There's TransDecoder.LongOrfs that is used to identify all candidate
ORFs.
(1b) search these using blast or pfam searches
2.  There's TransDecoder.Predict that does the final predictions,
optionally using the search results from (1b)

The new web documentation provides pointers for how to do the blast or pfam
searches, as well as directing users to the new
http://hpcgridrunner.github.io/ project to facilitate grid-level bioifx
computes needed for this.  Also, for those that are Trinotate (
http://trinotate.sf.net) users, the outputs from (1b) will be directly
suitable for upload into Trinotate.

The software build process is hugely simplified and the package itself has
been trimmed down to include only the essentials (cd-hit).


-- 
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>