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Multiple Sequence Alignment Of 3' Utr

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
alignment multiple utr
• 7,488 views • link
updated by Ram Ram • written by Ria • Ria

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?

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

3 answers

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.

• 4 views • link
updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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

• 0 views • link
written by Ria • Ria

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.

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updated by Ram Ram • written by Micans Micans

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.

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updated by Ram Ram • written by Ari • Ari

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

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written by Raul • Raul

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

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written by Andreas Andreas

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