How to find conserved sequence regions from aligned sequences?

Question

[Shashi Kanth]

Hey from alignment of HLA locus sequences how to get exact conserved sequence regions

is there any specific software/tool?

Answer 1

[David Langenberger]

You could use the UCSC Genome Broswer and activate the conservation tracks.

Example

[Shashi Kanth]

Thanks you..

Answer 2

[Biomonster]

Hi,

If by "conserved sequences regions" you mean http://en.wikipedia.org/wiki/Conserved_sequence you'll then need to do an alignment with HLA sequences from numerous individuals maybe with ClustalW or MAFFT (you can also use BioEdit - has an intuitive GUI, but it's a bit old) and see the exact sequences that are identical (if you use nucleotides) or synonimous (if you use the protein sequences).

If you're referring to something else, then please ignore my answer.

[Shashi Kanth]

Exactly I'm looking for this. Thanks for your suggestion.