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Old 10-21-2011, 09:40 AM   #1
Ashu
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Default Genome Annotation tips

Can any one give me some tips about genome anotation for big genome, which tools or pipelines are good
Thank you in advance,
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Old 10-21-2011, 11:17 AM   #2
Richard Finney
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You might want to give more details on your "big genome". Large genomic data? new species? what species? De-novo assembled?
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Old 10-21-2011, 11:27 AM   #3
FredericRaymond
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General advice: Read the supplementary material from published genome papers, compare their methods and find which one would be better for you project.
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Old 10-24-2011, 08:50 AM   #4
Ashu
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Thank you both for your reaction :-)
@Richard, it's size is 3 GB, de novo assembled from short read. I am trying to follow the ensemble gene build pipeline, but it is not very clear. I was just wondering how other people do it. I have also seen in literature that people follow the ensemble pipeline. If there is any other tip, that will be nice
@FredericRaymond, thank you, I have done that already, but it is very vague.
Thank you again
ashu
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Old 10-24-2011, 09:59 AM   #5
boetsie
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one program I know of is AUGUSTUS, but i've never used it myself
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Old 10-24-2011, 11:05 AM   #6
FredericRaymond
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I've used Augustus for the annotation of the Leishmania tarentolae genome. The software is built for prokaryotes, but we collaborated with the creator of the software to adapt it for Leishmania, which do not have introns. It performed pretty well.
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Old 10-24-2011, 02:23 PM   #7
boetsie
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Ehhh, i see a contradiction in your reply FredericRaymond, i think you meant that the software is for eukaryotes. The website (http://augustus.gobics.de/) says
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AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
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Old 10-25-2011, 04:51 AM   #8
Ashu
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Thank you all for the tip, Augustus was in my list, but I was focused on the ensemble Pipeline. I will give it a try and see if it is a good tool.
Thank you again,
cheers
Ashu
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Old 10-25-2011, 06:11 AM   #9
FredericRaymond
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You right boetsie. My mistake. However, the intron-less models can be built for Augustus.

FR
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Old 01-03-2012, 08:26 AM   #10
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how do you guys find possible introns on a gene? Which software do you use?
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Old 01-03-2012, 06:43 PM   #11
yumtaoist
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Genewise is used very frequently
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Old 01-11-2012, 06:34 AM   #12
Hobbe
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bbsinfo, there are (as far as I know) three ways to find introns.

1) You could do a spliced alignment of some kind of assembled transcripts/ESTs using for example Blat (if you are working in nucleotide space that is)
2) Get junctions from mapped transcripts using for example Tophat
3) Align known proteins to the genome using Genewise, Exonerate or perhaps Scipio.

Check out the suggested pipeline on the PASA homepage, it works well:
http://pasa.sourceforge.net/
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Old 01-12-2012, 04:35 AM   #13
gprakhar
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Quote:
Originally Posted by Ashu View Post
Thank you all for the tip, Augustus was in my list, but I was focused on the ensemble Pipeline. I will give it a try and see if it is a good tool.
Thank you again,
cheers
Ashu
Hello,

Did you use the Ensemble pipeline?
If yes can you provide a few details!

Regards,
--
pg
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