BACK TO CONTENTS   |    PDF   |    PREVIOUS

Title

 

 

 

 

PIR pairwise alignment - A slip up for signal peptides

 

Authors

Seetharaaman Balaji 1*, Rangaswamy Kalpana 2, and Santhosh J. Eapen1

 

Affiliation

1Bioinformatics Centre, Indian Institute of Spices Research, 2Guest Lecturer, Bioinformatics, Bharathiar University, Coimbatore-641046, Tamilnadu

 

E-mail*

blast_balaji@rediffmail.com; * Corresponding author

 

Article Type

Hypothesis

 

Date

received June 28, 2006; revised August 11, 2006; accepted August 12, 2006; published online August 14, 2006

 

Abstract

The ability to calculate the correct sequence alignment is crucial to many types of studies. The accuracy in alignment is critical in predicting gene ancestry, the number and location of point mutations, evolutionary distance and phylogeny. A study was conducted to test the biological significance of PIR pairwise alignment using 40 N-terminal signal peptides of different taxonomic origin and having various functions. Our results suggest that PIR pairwise alignment is not ideal for some proteins with N-terminal signal peptides, because it produces an erroneous alignment that lacks both statistical and biological significances. This communication discusses the shortcomings in the PIR pairwise alignment tool and calls for a cautious approach while using it for signal peptides.

 

Keywords

 

PIR; pair wise alignment; SSEARCH; signal sequence alignment

 

Citation

Balaji et al., Bioinformation 1(5): 188-193 (2006)
 

Edited by

William Perrizo

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.