i am going to retrieve upstream non-coding sequences of some Saccharomyces genes from Ensembl but i do not how i can do it considering i am a beginner in working with data bases, if possible someone help me..
Depending upon of the actual amount of genes you define with your "some" , you can go through two or more strategies
-If that "some" is high, I would go for a gff and/or gft Saccharomyces file that I will process with R and the package GenomicRange or even with my own code
-If that "some" is low, I would go to places such as the NCBI datababase that allow you to "Change the region shown". You look into the annotations, and select the desired region. Then you can save that file in any of the available formats
How do bioinformaticians actually annotate UTRs? Is there a software available for such application?
The species I am working on (oreochromis niloticus) have GENSCAN annotated reference genome. However, the UTRs were not annotated. I intent to annotate the UTRs myself. Any primers for me to know where should I start?