[maker-devel] Maker gene prediction

[Carson Holt]

You can supply ESTs from a related organism to the alt_est= option.  Note
this runs really slow because it has to be translated in all 6 reading
frames (target and query), and will be less sensitive (larger threshold
for alignments to become statistically significant). So if you have
protein evidence from a related species, use that instead of the EST
evidence from a related species.

With respect to accuracy, the alignment evidence that suggests the
annotation is also the experimental evidence that supports an annotations
accuracy (so it is kind of a circular argument).  But the alignment
evidence does provide a correlative measurement.  Things with lower AED
scores better match the evidence and should be considered as higher
confidence, while genes with higher AED scores represent genes that have
lower confidence (this correlation is very well supported across many many
organisms).  You should be aware of what is considered realistic with
genome annotation.  In general for newly sequenced organisms, a genome
wide accuracy of greater than 80% is considered extremely well annotated
(but can't directly be measured except retrospectively - i.e. once you
have a future more complete assembly and more experimental evidence to
compare to).  Only a handful of genomes that have legions of curators
working over a decade (drosophila for example) have accuracies of greater
than 90%.

--Carson



On 6/30/14, 4:18 AM, "Rajesh Reddy Bommareddy"
<rajesh.bommareddy at tu-harburg.de> wrote:

>Dear Sir/Madam
>
>I have a general question regarding gene prediction and annotation in
>Maker.
>
>For example, I have a new sequence of a yeast strain, and i have to
>predict and annotate the genome. Of,course i know EST's from the same
>organism will help me to predict the genes accurately, but when i want
>to use EST or RNA transcripts from a closely related organism, how can i
>do that in Maker and how accurate will be the prediction ?. Is  the
>produced prediction and annotation valid ? How do i check this ?
>
>Thank you and Regards
>-- 
>M.Sc. Rajesh Reddy Bommareddy
>Institute of Bioprocess and Biosystems Engineering
>Hamburg University of Technology(TUHH)
>Denikestrasse 15, 20171 Hamburg
>GERMANY.
>e.mail: rajesh.bommareddy at tu-harburg.de
>Phone:+4940428784011
>Mobile:+4917663673522
>
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