I'm looking for alternative software for gene and functional prediction, metabolic pathway construction and etc., is anyone willing to share their experience in yeast gene and functional prediction?
Oh~ I see it's for reference base.
I doubt my specie lack of similarity, even one of the partial genome of rhodotorula just with 2k++ genes for 20Mbp. Wandering, why gene bank accept it ? I'm thinking to use it as reference for mapping and as reference for genome sequence survey.
I'm wandering why CDS extract from GFF file by gffread, cufflinks not really similar to the GFF content. It extract single gene into few exon region with same header. It's cause problem to blast the result in batch.
Personally, i use augusutus or Maker2 for gene prediction. However, I'm stuck in GFF format after gene prediction. I manually extract 20 predicted gene from GFF file, blast it with EST and RNARef. Search again SwissProt, the result really not convincing although 90% hit >70% similarity. It lack gene slice information.
I'm try to find a way for large scale gene prediction and functional annotation by semi automation. Then, just verify those genes lack of confidence lvl manually.
I face problem to predict Ribosmal gene. My student mail not allow to access Rammer. RAPYD pipeline required collaborate with the the author in order to use it.
It's there any way i can learn how to train gene prediction from my species ?
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