[maker-devel] Maker

[Carson Holt]

MAKER can't annotate assembled transcripts.  It can only annotate genomic
sequence.  Transcript annotation is a very different problem.

Using a different species' genome would not produce annotation for your
transcripts, rather your transcripts would just be considered evidence for
annotating that species genome.  Your best option is probably just to use
BLAST to look for homology between species.  Do BLAST both ways and if
gene A in species 1 is the best hit for gene B in species 2 and vice versa
(reciprocal best hits), then you can consider them as being paralogous.
Also use the proteome from the related species when doing the BLAST
analysis (not the nucleotide transcripts).

--Carson
  

On 9/30/14, 6:51 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:

>
>
>Mark Yandell
>Professor of Human Genetics
>H.A. & Edna Benning Presidential Endowed Chair
>Co-director USTAR Center for Genetic Discovery
>Eccles Institute of Human Genetics
>University of Utah
>15 North 2030 East, Room 2100
>Salt Lake City, UT 84112-5330
>ph:801-587-7707
>
>________________________________________
>From: Alfons Weig [a.weig at uni-bayreuth.de]
>Sent: Tuesday, September 30, 2014 1:30 AM
>To: Mark Yandell
>Subject: Maker
>
>Hello,
>
>I have just sent a feedback via the Maker feedback form but received the
>following error message: Therefore, I send it vir regular mail:
>
>Error executing run mode 'feedback': Can't call method "MailMsg" without
>a package or object reference at /var/www/cgi-bin/mwas/lib/MWS.pm line
>1116.
>at /var/www/cgi-bin/mwas/maker.cgi line 21.
>
>I have just tested the Maker annotation pipeline with short sequences
>from an RNAseq de-novo assembly using A. mellifera as areference genome.
>Unfortunately, honey bee is not the species we sequence but is closely
>related to it.
>I was wondering whether this was a good approach? There are no genome
>data availabe for our bee species. Is maker able to annotate de.novo
>assemble mRNA transcripts obtained by Velvet/Oases (including partial
>sequences)?
>
>Best regards
>Alfons Weig
>
>
>Dr. Alfons Weig
>DNA-Analytik & Ökoinformatik - Univ. Bayreuth - NW1
>Universitätsstrasse 30
>95447 Bayreuth - Germany
>Tel. +49 (0)921-552457
>www.daneco.uni-bayreuth.de
>