single_exon parameter

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single_exon parameter

Khan, Anar
Hi
 
I see that “single_exon” is set to zero by default, and read in the tutorial:
 
single_exon - tells MAKER to consider single exon EST evidence when generating annotations. Single exon ESTs are more likely to be genomic contamination.
 
For a species which is related to my fungus of interest the average number of exons per transcript was reported to be ~2.9 (this based on predicted genes). I think it’s likely there are many single exon genes in my genome and I’m wondering whether kicking out the single exon ESTs is a bit stringent. I see the rationale for treating single exon ESTs as contamination, but I’m wondering if this applies to genomes containing fewer exons per gene on average. Does anyone have advice on adjusting this parameter (together with the single_length param)?
 
Also does single_exon apply to altest evidence as well?
 
Cheers
Anar
 
 
____________________________
Anar Khan
Bioinformatician
T +64 3 489 9154
E anar.khan@agresearch.co.nz
 
AgResearch Limited
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel, New Zealand
T +64 3 489 3809   F  +64 3 489 3739  www.agresearch.co.nz
 
Farming Food and Health. First
Te Ahuwhenua Te Kai me te Whai Ora. Tuatahi
 
 
 
 

 


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Re: single_exon parameter

Carson Hinton Holt
Re: [maker-devel] single_exon parameter Sorry for the slow response, I’ve been out of town for two weeks.

single_exon=0 works for most cases; however for organisms like fungi and oomycetes which have few introns, you should set single_exon=1, also set single_length to throw away short single exon ESTs.  When annotating the oomycete Pythium ultimum (lots of single exon genes), we were able to show that 95% of ESTs over 250 bp in length corresponded to genes.  You can set this to a higher or lower number depending on the quality of your cDNA and repeat content of the organism (lots of repeats means lots of false alignments). Pythium ultimum had 5-7% repeat content for comparison.

Single_exon afffects est and altest.

Thanks,
Carson

On 6/8/11 5:56 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi
 
I see that “single_exon” is set to zero by default, and read in the tutorial:
 
single_exon - tells MAKER to consider single exon EST evidence when generating annotations. Single exon ESTs are more likely to be genomic contamination.
 
For a species which is related to my fungus of interest the average number of exons per transcript was reported to be ~2.9 (this based on predicted genes). I think it’s likely there are many single exon genes in my genome and I’m wondering whether kicking out the single exon ESTs is a bit stringent. I see the rationale for treating single exon ESTs as contamination, but I’m wondering if this applies to genomes containing fewer exons per gene on average. Does anyone have advice on adjusting this parameter (together with the single_length param)?
 
Also does single_exon apply to altest evidence as well?
 
Cheers
Anar
 
 
____________________________
Anar Khan
Bioinformatician
T +64 3 489 9154
E anar.khan@agresearch.co.nz

AgResearch Limited
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel, New Zealand
T +64 3 489 3809   F  +64 3 489 3739  www.agresearch.co.nz <http://www.agresearch.co.nz>

Farming Food and Health. First
Te Ahuwhenua Te Kai me te Whai Ora. Tuatahi

 
 
 
 


Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.





Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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