SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Next-generation DNA sequencing-based assay for measuring allelic expression i Newsbot! Literature Watch 0 10-23-2011 03:40 AM
Very short contigs and short isotigs of newbler output. kentnf 454 Pyrosequencing 3 09-27-2011 07:54 AM
ChIP-Seq: A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detec Newsbot! Literature Watch 0 05-03-2011 03:00 AM
PubMed: Comparison of bisulfite sequencing PCR with pyrosequencing for measuring diff Newsbot! Literature Watch 0 10-20-2009 03:00 AM

Reply
 
Thread Tools
Old 01-27-2012, 05:35 AM   #1
turnersd
Senior Member
 
Location: Charlottesville, VA

Join Date: May 2011
Posts: 112
Default Measuring conservation for short motif

How can I measure sequence conservation among different species for a very short (5-8 nt) motif in introns?

I know I can visualize conservation in UCSC, but I want something more quantitative. I'm looking at RNA-binding protein recognition motifs that occur in introns flanking the alternative exon. I want to show that this motif is more conserved than a "normal" intron. This paper did it, but didn't really tell how:

Quote:
We analyzed sequence conservation of pentamers in the mouse intronic regions to identify potential splicing regulatory elements. The mouse introns were aligned to 7 other mammalian genomes that have at least 5x coverage in the UCSC 28-way multigenome alignment. For each pentamer in each region [upstream and downstream of exon], a conservation rate (CR) was calculated as the fraction of aligned and conserved occurrences among total occurrences. The significance of CR of each pentamer is evaluated by comparing with 10 other pentamers with similar expected CR calculated using the first-order Markov model. This procedure essentially controls for possible sequence bias in the dataset. A P value was calculated by using the binomial distribution.
Thanks in advance!
turnersd is offline   Reply With Quote
Old 11-06-2014, 04:47 AM   #2
priya
Member
 
Location: sweden

Join Date: Apr 2013
Posts: 57
Default

Quote:
Originally Posted by turnersd View Post
How can I measure sequence conservation among different species for a very short (5-8 nt) motif in introns?

I know I can visualize conservation in UCSC, but I want something more quantitative. I'm looking at RNA-binding protein recognition motifs that occur in introns flanking the alternative exon. I want to show that this motif is more conserved than a "normal" intron. This paper did it, but didn't really tell how:



Thanks in advance!
Hi,
May I know did you find out the answer to your post. Now I am struggling with the similar question. I have short motifs and would like to check those are conserved across few species. Please let me know if you have any suggestion how to do it.

Many Thanks
priya is offline   Reply With Quote
Reply

Tags
conservation, sequence comparison

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 03:15 PM.


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