Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum

Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum (http://www.molecularstation.com/forum/)
-   Bioinformatics (http://www.molecularstation.com/forum/bioinformatics/)
-   -   Global or local alignmnet (http://www.molecularstation.com/forum/bioinformatics/86678-global-local-alignmnet.html)

exutu 10-23-2012 07:07 AM

Global or local alignmnet
 
Hi :)
I'm doing a project where I need to align three domains (pairwise i.e. 3 different alignments).
The domains have the length of 116, 118 and 124 amino acids, so they are about the same size.
I ran both a local and a global alignment via EMBOSS (default values and used needle for global and water for local).
The local alignment gave the best result (i.e. lowest gap % highest similarity and identity % for all sequences).
However I thought that when you were interested in getting the best alignment of a full sequence that global would be the appropriate choice.
I'm new to bioinformatics so some of my assumptions may be way off. Please help me choose the correct method.

Rokib 11-24-2012 07:28 PM

Re: Global or local alignmnet
 
Oh that is great.
I like your opinion dear.


All times are GMT. The time now is 03:24 PM.

Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved

Page generated in 0.08870 seconds with 11 queries