Multiple Sequence Alignment Of 3' Utr
3
2
Entering edit mode
11.1 years ago
Ria ▴ 20

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 • 4.9k views
ADD COMMENT
2
Entering edit mode

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?

ADD REPLY
2
Entering edit mode
11.1 years ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
9.2 years ago
Micans ▴ 270

It's been a while since I looked at this, but we have used LAGAN to align UTRs (http://lagan.stanford.edu/lagan_web/index.shtml). It is optimized for non-coding, and other poorly conserved regions of the genome.

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode
9.2 years ago
Raul • 0

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2453 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6