I am working on Black fly. I just received the genome fasta file. I want to find the odorant binding protein in the genome. Which software should I use? And who should I consider as my reference model? I was thinking of using drosophila as a reference. Is there a conserved domain that I can search for in the genome?
Hello Min, thank you so much for your answer. Can you please tell me if I can find a receptor based on the same information? I am really new to Bio-informatics. Thanks again!
Hey Amruta,
I've been working with antennal bee transcriptomes to detect OBPs and it is very straight forward to use blast. However, the OBPs are interrupted by introns in the genome what makes it actually more complicated to detect the genes. A good start might be e.g. this recently published paper by Obiero et al.
http://www.ncbi.nlm.nih.gov/pubmed/24763191
They used a blast approach combined with methods to detect and refine exon-intron boundaries.
Hope this helps,
Philipp
Send me your genome fasta file to see what I can do for you.
Do you have raw shotgun data? I have scripts to get genes out of raw reads.
https://github.com/rachelss/GFR
I am going to recieve the raw data soon. I will try your scripts soon.
Thank you all for your awesome support.
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