Multiple Sequence Alignment Of 3' Utr

Question

[Ria]

how can we do multiple sequence alignment of the 3' UTRs of the species analyzed and obtaine the result for CYP17A1 9606 like this

AGGCUGUAACUCACAGCCCCUG--UCCACCCUAUG---UGGC-CCCACAACACAGAUUUAGAGAUACAACCCCCCACCCUUCUCCGCCAUUCUUCCCUACUCCCAACCCACUCUGCCUUCUUUUUCAGCUUGUGG-CAAUGCCAGUGAUG-UGCAUAAACAGUUUUUUUUUUU

[Giovanni M Dall'Olio]

I don't understand which is the real question. Do you need a way to find all the 3'UTR of the species? Or are you asking for a method to do alignment?

Answer 1

[Giovanni M Dall'Olio]

Go to Ensembl-BioMart. Select the latest ensembl release and the organism of your interest. If it is not there, look at the other BioMart installations.

After doing that, go on 'Attributes' and in the 'Sequences' section, select the 3'UTR along with the sequence length you want to study.

Then, for doing the alignment, you can use a tool like T-coffee or clustalw... have a look at the other questions on this site to see opinions on different multiple alignment softwares.

[Ria]

thanks for your help i will follow wat u said.hope i get my answer

Answer 2

[Micans]

It's been a while since I looked at this, but we have used LAGAN to align UTRs. It is optimized for non-coding, and other poorly conserved regions of the genome.

[Ari]

You could also try PAGAN with the option --454. That models homopolymer errors in pyrosequencing data but it should also work with highly repetitive 3'-UTRs.

Answer 3

[Raul]

Hello, I am working with 3'-UTR sequences and I need goods alignments of these 3'-UTRs. Actually a am using mafft-xinsi. Somebody know a best way to align these kind of sequences. Thanks

[Andreas]

Mafft Xinsi is a very good choice if you know that your sequences are structurally conserved, with little sequence homology.