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Global or local alignmnet

Global or local alignmnet - Bioinformatics

Global or local alignmnet - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 10-23-2012, 07:07 AM
Pipette Filler
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Default 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.
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Old 11-24-2012, 07:28 PM
Pipette Filler
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Default Re: Global or local alignmnet

Oh that is great.
I like your opinion dear.
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