multi-species sequence alignment

Question

[tomastokar]

Hi all,

I have a single 5000bp promoter sequence of a human gene, and would like to do a multi-species sequence alignment to look for conservation. I did some search, but I wasn't able to find any computational tool that would do the thing. I am very new to this topic, I have never done any sequnce aligment before. Could you please give me any advice, how should I proceeed?

Thanks a lot.

T

[tomastokar]

Hi again,

Thanks a lot for your advice, both of you. Now I would like to ask if there is any way to process the multiz results from genome browser into a publication-quality graphics?

Thanks a lot in advance.

T

[Pierre Lindenbaum]

Ask this as a new question please.

[Asaf]

You can take a print screen of it (or export to PDF and cut) I've seen Genome Browser snippets in papers before

[tomastokar]

Hi again and thanks for suggestion. I am looking for something similar to subfig B of this:

http://cancerres.aacrjournals.org/content/71/1/277/F5.expansion.html

Thanks a lot for any advice.

[tomastokar]

Thanks a lot for your advice, both of you.

Answer 1

[Prakki Rama]

For clustering, you need to have multiple sequences from different species. Find the same gene you have in different species.Try running clustalw/x

Answer 2

[Asaf]

If you have no experience I would recommend using previous work (which I always prefer, even if I have experience with something). The UCSC genome browser would be a great place to find what you need. Start by locating your sequence (either by looking up the region or finding it using BLAT) and then make sure that the conservation track under the Comparative Genomics section if in full mode, in the browser you would be able to find similar sequences under the "multiz alignment of 100 vertebrates" track, click on it to get more information.