[maker-devel] Maker with Augustus

[david.swarbreck]

Thanks carson and congratulations on the new arrival. I plan to generate 
the evidence alignments (using maker and other tools) prior to running 
maker for the final gene build is there any disadvantage at all in 
feeding in GFF rather than fasta sequences? Is it necessary to provide 
the blastx hits as well as the polished protein2genome alignments?

Also does maker utilize the target tag information i.e. the transcript 
relative positions, I notice the maker protein/nucleotide GFFs include 
this but I'm wondering if I need to add this info for alignments 
generated outside of maker. One final question regarding the 
stringencies for the blast runs how dangerous is it to alter the default 
parameters, i.e is loosening these highly likely to be detrimental to 
the gene build. From 146,022 protein sequences in genbank (same phylum 
as the genomic sequence) only 17386 were aligned under the default 
parameters in Maker.

Regards
David

Carson Holt wrote:
> Sorry for the slower than average response. My wife went into labor 
> over the weekend.
>
> For the initial training of augustus, you can either select an 
> existing organism or do the training yourself. Once augustus is 
> trained, MAKER will produce both the ab initio gene predictions 
> (without hints) and hint based predictions for you. You don’t have to 
> worry about building the hints file. MAKER does that for you based on 
> alignments produced from the EST and protein evidence you provided in 
> the maker_opts.ctl file. Just make sure you set the 
> AUGUSTUS_CONFIG_PATH environmental variable in your profile per the 
> augustus install instructions.
>
> I hope that answers your question. If not let me know.
>
> Thanks,
> Carson
>
>
> On 10/15/09 12:29 PM, "david.swarbreck" <dswarbreck at stanford.edu> wrote:
>
>     Hi,
>
>     I have a question relating to using Augustus as the predictor with
>     Maker. From looking at the documentation for augustus the hints files
>     detailing aligned features uses a non-standard GFF format. These
>     include
>     the use of non SO compliant features such as exonpart (treated
>     differently to exon by augustus) and the inclusion of a source
>     identifier in col9 which has to be specified in the augustus
>     config. In
>     addition in the standalone Augustus setting a bonus and penalty is
>     required for obeying a hint feature.
>
>     So my question is when using Augustus as the predictor in Maker is
>     Maker
>     taking care of this for me or do i still need to define exonparts as
>     distinct from exon and provide bonus and penalty information. Is
>     there a
>     particular GFF3 format which maker requires to define for example
>     alignments e.g can these use the match type (e.g. EST_match), can this
>     use the cigar format or should these features be described as exons.
>
>     Any help appreciated
>     david
>
>
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>

-- 
************************************
David Swarbreck
The Arabidopsis Information Resource
Carnegie Institution of Washington
Department of Plant Biology
260 Panama St.
Stanford, CA 94305
U.S.A

E-mail dswarbreck at stanford.edu
www.arabidopsis.org/about/staff.jsp
************************************