Pipeline suggestions for gene detection
Hi everybody!
I've been searching this question through the internet and forum but I didn't find an answer.
I'm working with a non annotated (Scaffold stage) genome (Leptinotarsa decemlineata or Colorado Potato Beetle). I want to know if a receptor from a close specie (Tribolium castaneum) wich is annotated and thus, available in FASTA, is within Colorado Potato Beetle genome. I want to know this because, in that case, I would want to silence it using mRNAi.
So I think the first step is to run a BLAST, wich I already ran, and find if there is homology, wich I found in two scaffolds.
From here, and sorry for bother you with my naive questions, I do not know what to do to finally get a presumptive mRNA(CDS) and/or information about introns and exons.
My actual question is: Can you suggest me any pipeline using the appropriate bioinformatic tools to get that mRNA?
Thank you in advance!
I've been searching this question through the internet and forum but I didn't find an answer.
I'm working with a non annotated (Scaffold stage) genome (Leptinotarsa decemlineata or Colorado Potato Beetle). I want to know if a receptor from a close specie (Tribolium castaneum) wich is annotated and thus, available in FASTA, is within Colorado Potato Beetle genome. I want to know this because, in that case, I would want to silence it using mRNAi.
So I think the first step is to run a BLAST, wich I already ran, and find if there is homology, wich I found in two scaffolds.
From here, and sorry for bother you with my naive questions, I do not know what to do to finally get a presumptive mRNA(CDS) and/or information about introns and exons.
My actual question is: Can you suggest me any pipeline using the appropriate bioinformatic tools to get that mRNA?
Thank you in advance!