[Jalview-discuss] Saving Motif Patterns?

[Dobbs, Mike]

Thanks Jim. I will look forward to the next release.

We are needing this option to help evaluate multiple protein alignments with typically 10 to 50 related seqs. We look for regions of interest using quite a few different regular expression patterns. Exact search matches don't find all the cases we're after. We do this type of work regularly in a modest throughput mode, looking for the same patterns again and again.

We have been using GeneDoc to do this kind of work, but it is quite out of date and needed lots of modifications to work right for this.

Thanks.
Mike.

From: Jim Procter [mailto:foreveremain at gmail.com] On Behalf Of Jim Procter
Sent: October-19-10 11:50 PM
To: Dobbs, Mike
Cc: 'Jalview-discuss at jalview.org'
Subject: Re: [Jalview-discuss] Saving Motif Patterns?

Hi Mike

On 20/10/2010 01:02, Dobbs, Mike wrote:

Hello,
I'm new to Jalview and this mail list.
I'm wondering if it is possible to enter a list of regular expressions for motifs I'm interested in and have them saved. This way I can then re-apply the list to my next multiple alignment without needing to manually enter the expressions one by one. I have about 10 I need to look for all the time.
Oops - I got hit by a rather bizarre 'feature' of thunderbird then - the text of your email got inserted into a reply email assigned to the thread started by Eric (more coffee needed by me I think!). For convenience, I've repeated the reply below:


Jalview doesn't do this at the moment, but it's a useful

useful feature request - so I've added it to the list

(http://issues.jalview.org/browse/JAL-684).



Jim.



ps. Just as an aside - are you annotating regions of the same sequences in different alignments ? If that is the case, then after annotating them all for one alignment using the Find/Create features button, simply export the annotation as a 'features file', and then drag it on to the next alignment to mark up the same regions again.



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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group

Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk

The University of Dundee is a Scottish Registered Charity, No. SC015096.
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