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Multiple sequence analysis of polygalacturonases and invertases and phase shift in conserved motifs

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Field Value
 
Title Multiple sequence analysis of polygalacturonases and invertases and phase shift in conserved motifs
 
Creator Palanivelu, P
 
Subject ClustalW
conserved motifs
DIALIGN
invertases
MAFFT
phase shift
polygalacturonases
T-COFFEE
 
Description 24-30
Multiple sequence analysis by programs, such as ClustalW and T-COFFEE, is one of the important tools in bioinformatics. These programs are used to predict conserved motifs among related or unrelated proteins and nucleic acids that are of functional importance. However, it is observed that the conserved motifs in protein sequence analysis from some organisms especially from archae bacteria, extremophilic organisms and fungi do not align with other conserved sequences all the time and the conserved motif(s) in these organisms may be slightly shifted, either side of the conserved motif aligned for all the other organisms. Even one protein sequence is not aligned with others; the ClustalW or T-COFFEE does not mark the whole block as the conserved motif even though the particular motif is conserved among others. This is a serious problem as the investigator may miss important and functional motif(s) because of such misalignments. But a careful manual analysis of the aligned sequences will solve such anomaly. This is substantiated with two examples; one from polygalacturonase sequences analysis and the other from invertase sequences analysis using ClustalW, T-COFFEE, DIALIGN and MAFFT algorithms.
 
Date 2009-02-10T04:04:03Z
2009-02-10T04:04:03Z
2007-01
 
Type Article
 
Identifier 0972-5849
http://hdl.handle.net/123456789/3007
 
Language en_US
 
Relation Int. Cl.⁸ C12N9/26, 9/38, 9/40
 
Publisher CSIR
 
Source IJBT Vol.6(1) [January 2007]