SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
rare cancer mutation detection pipeline dietmar13 Bioinformatics 14 04-09-2014 10:32 PM
Mpileup/BCFtools pipeline not picking up indels (suggestions please) cam.jack Bioinformatics 7 05-17-2013 01:05 PM
Suggestions for examining Nif gene diversity in soil and root?? ramsemm Illumina/Solexa 0 10-26-2012 12:34 PM
Looking for positive selection pipeline suggestions JueFish Bioinformatics 0 09-25-2012 08:23 AM
Looking for a pipeline - SV detection mit mate pair tristanstoeber Illumina/Solexa 0 02-17-2012 04:24 AM

Reply
 
Thread Tools
Old 01-15-2014, 03:09 PM   #1
Galo
Junior Member
 
Location: Valencia, Spain

Join Date: Dec 2013
Posts: 9
Lightbulb 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!
__________________
To do is to be (Nietzsche) - To be is to do (Kant) - Do be do be do (Frank Sinatra)
Galo is offline   Reply With Quote
Reply

Tags
find, gene, mrna, pipeline

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:49 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO