Beyond Bioinformatics

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

Edited by

William Perrizo

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.