I would like to find regions with a high conservation of among about 30-40 DNA sequences. Sequences aligned with MEGA v.6. How can I do this? What software should I use? Is it necessary to be align sequences already? Thanks.
You can estimate varibility of your sequences by simply providing alignment (by clustalW for example). But a lot of regions in different genomes are already analized for conservancy. So you also must to study liretature on your topic
Depending on the type you problem you have, but some ideas:
- multiple align them and take a look at alignment; if you have lots of sequences, it might be mess, but it is good way of evaluating conservation among all of your sequences; also consider trying couple of different tools and comparing them; it will be of less use if your sequences are very long or if you are interested in conservation among some rather then all sequences
- MEME (http://meme.nbcr.net/meme/cgi-bin/meme.cgi) tends to provide decent results for (short) conserved motifs
- for longer sequences, searching them against known databases (BLAST vs RefSeq or UniProt) might reveal if they have some common motifs that already appear elsewhere
If its a protein coding gene... convert to ORFs and go for Shannon entropy analysis...
you can compare your entropy with reference multiple alignment too...
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