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Old 01-08-2014, 02:29 AM   #1
papori
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Location: berd

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Default exon-intron prediction, invertebrate

Hi all,
We sequenced the genome and the transcriptome of a non-model invertebrate
We made denovo assembly for both.
Now, we have 1000's of scaffolds + 1000's of transcripts.
We want to use this information for getting the full picture of some gene of interest.
For example, we have Transcript X which isnt full length, we want to find the rest of it in the genome.

What we thoght about is to first find which are the exons/introns in the genome, and then to search for the rest of the desire transcript.

I used ORF finder, but the output is too complicated when the input is 50K bp.
I also used AUGUSTUS, but my organism inst in there list so i used C-elegans, and the output didnt have any match using blast.

Any ideas will be meaningful..

Thanks,
Pap
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Old 01-09-2014, 04:02 AM   #2
TiborNagy
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Posts: 329
Default

We have used Pasa for tasks like this.
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