[maker-devel] Maker protein match & tandem similar genes

[Tim Fallon]

Hi Carson,

Thanks for the response! After sending my initial email, I did notice this particular issue was warned about in the Cambell et al. 2014 Maker protocols paper.  Perhaps future versions of the pipeline might have a workaround or warning for this presumably common issue. At least in my case, the genome I’m annotating has large introns, and also tandem gene clusters of homologous genes, so I’ve been unable to solve this issue entirely by changing existing parameters (e.g. split_hit), though perhaps exonerate / protein2genome direct gene annotation does handle it correctly.

Regarding the protein2genome only being a intermediate stage, as I’ve been working towards a final annotation, I’ve actually been mostly relying on the protein2genome direct gene annotation, as although I have a trained Augustus that is presumably getting the hints from the evidence, my main target genes have been producing subtly wrong gene-models (Augustus produced splice sit off by a handful of nucleotides, leading to unintended & unsupported amino acids in the protein).  I also trained SNAP, but those predictions were worse than the Augustus predictions.

Do you have any tips for using the Evidence Modeler integration of the Maker 3.0.0 beta?  That seems to be the best way to have the final gene models rely more on extrinsic evidence over my mildly incorrect ab-initio predictions.  Or perhaps PASA is more appropriate for gene-models that would strictly adhere to extrinsic de novo assembled transcript / predicted ORF evidence?

All the best,
-Tim

> On Jun 23, 2017, at 12:27 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> The protein_match features are the direct BLASTX results. Because of how BLAST works, if you have neighboring paralogs, it can place HSPs in both. So the final hit ends up being to large. The protein2genome feature is then the result of exonerate polishing these blast alignments (this will usually remove false merging and bad exon order). The protein2genome=1 option on the other hand just tell maker that you want to try and convert the exonerate hits directly into gene models (only do this for training and not final annotation). One way to drop the BLASTX results may be to filter the GFF3 results to keep only protein2genome features, pass those into protein_gff, and then turn off protein= for the next run. This forces the blastx results to be dropped. You may want to set blast_depth parameters to something like 10 in maker_bopts.ctl before doing this to trim per locus evidence depth to 10 if you are using too much input data.
> 
> —Carson
> 
> 
> 
>> On Jun 13, 2017, at 11:35 AM, Tim Fallon <tfallon at mit.edu <mailto:tfallon at mit.edu>> wrote:
>> 
>> Hi there,
>> 
>> I am aligning reference proteins to an insect genome through Maker, in preparation for using the gene models from the protein alignments as evidence to train SNAP (alongside de-novo assembled RNA-Seq).  I also plan on passing the protein alignments to a future Maker run as hints for SNAP / Augustus.
>> 
>> I’ve noticed that the maker blastx "protein_match” feature, which I presume is a result of Maker trying to make the blastx HSPs contiguous to format as a reference for exonerate (this Maker run did have protein2genome turned on), tends to fuse tandem genes from the same gene family.  See attached image.
>> 
>> The red regions highlight two de novo assembled transcripts which I aligned manually, from two genes that are homologous.  The top track is the blastx “match_part” features, the bottom track is the blastx “protein_match” features.  You can see that the protein_match fuses the two genes, using ~1000 bp in an intervening region, that doesn’t have blastx HSP support in the blastx “match_part” track.  The trick seems to be that a single reference protein, has blastx matches on both the left and right gene.
>> 
>> Cleary this isn’t a good gene model to train SNAP with, but would this misannotation screw up the hints passed to pretrained SNAP / Augustus?
>> 
>> Is there anyway to prevent this protein_match fusing of adjacent similar genes from happening?  For species that are closer, I’ve set the “eval_blastx” to be a lot higher (1e-50), and in that case the genes don’t get fused (but, with that level of stringent search, it is more like an orthology search, rather than just annotating general protein similarity).  I do have (rare) introns ~1000 bp, so I wouldn’t want to change the Maker “split_hit” parameter to be too low.
>> 
>> All the best,
>> -Tim
>> 
>> Timothy R. Fallon
>> PhD candidate
>> Laboratory of Jing-Ke Weng
>> Department of Biology
>> MIT
>> 
>> tfallon at mit.edu <mailto:tfallon at mit.edu>
>> 
>> <protein_match_example.png>
>> 
>> 
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> 

Timothy R. Fallon
PhD candidate
Laboratory of Jing-Ke Weng
Department of Biology
MIT

tfallon at mit.edu

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