Can anyone recommend software for annotating novel transcripts/genes from Tuxedo

[gwilymh]

Hi,

I am running RNASeq experiments and identifying and quantifying novel genes and transcripts using a Tudedo pipeline (Bowtie--> TopHat--> Cufflinks--> Cuffcompare--> Cuffmerge--> Cuffdiff). I am looking to annotate the novel genes, transcripts and isoforms from the GFF files output by the Tuxedo suite. If possible, I also wish to get a class of students onto the annotation process also.

Is there any software that can be used for such large-scale genome annotation? (I have tried using Apollo but it will not open GFF files in a windows environment).

[sdriscoll]

Best is can suggest is to use a utility to fetch the sequence of the novel features (Tophat provides gffread for this...try gffread -h for help) and then use NCBI's blast to find hits with known gene features. It's kind of a one-at-a-time thing so maybe that's perfect for an army of students.

[Wallysb01]

Do a gff to fasta conversion (prefearably after removing the known genes), then run the sequences through blast2go. That works fairly well and won't require an army of students, but rather a lot of CPU-hours (assuming its a lot of novel transcripts).