Measuring conservation for short motif

[turnersd]

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:

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!

[priya]

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