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Is There Any Tools/Methods For PacBio IsoSeq New gene prediction analysis?
We have used the SMRT(Pacific Biosciences) sequencing system PacBio RS II to generate cDNA sequences. After isoform-level clustering, polishing and trimming of raw data, non-redundant contigs were obtained. Also with MatchAnno, we have got the isoforms's annotiations? But there still some isoforms located outside of the known genes, so we want to do the new gene prediction analysis. But the tools we found can only be used to analysis the short reads or the short+long reads. So is there any tools do the analysis with only pacbio Iso-seq data?
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happy -
You can basically treat the Iso-Seq output as an assembled transcriptome using second generation sequencing, or EST using sanger.
So tools like transdecoder, trinotate, and PASA are useful. -
To predict new gene functions there are a few ideas besides what BoHan said:
--- plain BLAST to NR to find homologs
--- PFAM or protein domain searches
(you can try using ANGEL [https://github.com/PacificBiosciences/ANGEL] to translate first into ORF)
There's also a tool called BLAST2GO (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375974/) but I haven't used it myself. The author Ana Conesa (U Florida) is actually developing a new pipeline for Iso-Seq for functional annotation, but it's not quite on the market yet...Comment
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I‘ll have a try. Thanks a lot(∩_∩)O~happyComment
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