[maker-devel] Mapping gene names

[Carson Holt]

I need to fix that last update tag.  I did a point release, because there
were a couple of very minor fixes that didn't justify a full release (tRNA
naming and a fasta_merge bug for tRNAs - I think three lines total of code).
There won't be another major version release for a while because we're
working on MAKER-EVM which will be version 3.0 (joint project for full MAKER
integration with EVM).  So just point releases on 2.31 (which will be the
very last version of MAKER2).  I'll fix the static link and add an new one
for 2.31.3.

--Carson


From:  Shaun Jackman <sjackman at gmail.com>
Reply-To:  Shaun Jackman <sjackman at gmail.com>
Date:  Friday, May 2, 2014 at 2:00 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Mapping gene names

Fantastic. Thanks, Carson. I didn’t realize that there was a point release
of MAKER. It’s not announced on the MAKER home page, which still reports
Last Software Update v2.31 (Feb 11, 2014). Where are point releases
announced?

The static link for MAKER 2.31
<http://yandell.topaz.genetics.utah.edu/maker_downloads/static/maker-2.31.tg
z>  reports 403 Forbidden. Is there a new static link for MAKER 2.31.3?

Cheers,
Shaun



On 2 May 2014 12:50, Carson Holt <carsonhh at gmail.com> wrote:
> That should already be fixed in the current 2.31.3 download. I'll also send
> you the subversion credentials in a separate e-mail.
> 
> Thanks,
> Carson
> 
> 
> From:  Shaun Jackman <sjackman at gmail.com>
> Reply-To:  Shaun Jackman <sjackman at gmail.com>
> Date:  Friday, May 2, 2014 at 1:40 PM
> 
> To:  Carson Holt <carsonhh at gmail.com>
> Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Mapping gene names
> 
> Hi, Carson. Do you happen to have a patch that I could test out that fixes the
> naming of the tRNA identified by tRNAscan?
> 
> Is the MAKER subversion repository public, and if so, what’s its URL?
> 
> Cheers,
> Shaun
> 
> Shaun wrote…
>> 
>> The integration of MAKER-P with tRNAscan is very useful. The identified genes
>> are named e.g. trnascan-205522-processed-gene-0.38.  tRNA genes are
>> conventionally named according to the amino acid and anticodon, such as
>> trnW-CCA. Would it be possible for MAKER to name or perhaps prefix the names
>> with that convention?
> 
> On 6 March 2014 12:58, Carson Holt <carsonhh at gmail.com> wrote:
> 
>> Yes.  I’ll fix the naming.
>> 
>> Thanks,
>> Carson



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140502/38f70263/attachment-0003.html>