Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
synonymous snps from vcf bioinfun Bioinformatics 15 09-19-2017 06:41 AM
determining if a SNP is synonymous or not nlsullivan Bioinformatics 6 10-13-2013 05:38 AM
Nucleotide to amino acid translation + synonymous/non-synonymous count Darth Ghisus Bioinformatics 2 09-04-2012 04:15 AM
how to tell SNPs synonymous v. nonsynonymous Margot Bioinformatics 31 09-29-2011 09:24 AM
Non synonymous SNP programs colindaven Bioinformatics 9 05-15-2010 10:50 PM

Thread Tools
Old 03-15-2013, 01:17 PM   #1
Junior Member
Location: Italy

Join Date: Mar 2013
Posts: 6
Default estimation of non synonymous over synonymous (Ka/Ks) SNPs over genome with RNAseq

dear all
I performed RNAseq in closely related plant species and was asked to perform a Ka/Ks estimation of the transcriptome. The problem is, that a number of genes are not fully covered, so I was wondering just to consider just those who are 100% covered. However, in some papers it seems that people look at single codons, not whole CDS, so the question is: do I consider the first option or the second is correct as well? Clearly, if I would consider also genes with incomplete coverage, I could get higher numbers. In case, does anyone can suggest me a software?
Many thanks
piemmea is offline   Reply With Quote
Old 05-25-2014, 10:32 PM   #2
Senior Member
Location: USA

Join Date: Apr 2010
Posts: 102

I don't know if it is too late for you but i recently did something in the lines that you mentioned above - using RNA-Seq data to calculate Ka/Ks ratio for two genomes. For this first i have reconstructed the genomes of these species by incorporating the SNPs and then used KaKs calculator ( to calculate Ka/Ks ratio. Let me know if you need further details. Good luck!

upendra_35 is offline   Reply With Quote

ka/ks, synonymous snps

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 06:02 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO