hello
i did NGS on olive flounder and i got a list of microrna for different time point. now i need to do the target prediction of these microrna. the problem is the olive flounder don't have a published genome and also i couldn't find the 3'UTR of it in UCSC genome browser. the only solution is to get the genes of olive flounder from NCBI database and retrieve their 3'UTR.
can someone help me in this procedure?
thank for your help.
I had the same problem during my NGS analysis of small RNAs in Penicillium chrysogenum. In addition, working with this fungus makes target gene prediction even more complicated due to the fact that there is no tool desinged for fungal miRNAs-like RNA target prediction. If you have the genomic sequence with gene annotation but without informations of your UTRs you should use the expected 3'-UTR of about 300-1,000 bp. For this, you need the complete or partial genome sequence. IMO this is all you can do without generating EST data. Maybe you should take a look at Shao et al. 2015 (DNA Research, doi: 10.1093/dnares/dsv001) for the genome sequence of your flounder and my work from 2015 for the bioinformatic procedures (PLoS One, doi: 10.1371/journal.pone.0125989).
hello Pr.Tim Alexander Dahlmann i read the articles, for olive flounder genome there wasn't any link to it in Shao paper and also there isn't any gene annotation.
thanks a lot for your help.
- Badges
- Science topic
- Similar topics
- Biological Science
- Immunology
- Antibodies