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© Oxford University Press

Multiple alignment of sequences on parallel computers

Shashank Date , Rajendra Kulkarni , Bhavana Kulkarni , Urmila Kulkarni-Kale 1 and A.S. Kolaskar 1,2

Center for Development of Advanced Computing, DIC, Department of Zoology, University of Poona Pune 411 007, India
1Center for Bioinformatics, DIC, Department of Zoology, University of Poona Pune 411 007, India

2To whom reprint requests should be sent

A software package that allows one to carry out multiple alignment of protein and nucleic acid sequences of almost unlimited length and number of sequences is developed on C-DAC parallel computer—a transputer-based machine. The farming approach is used for data parallelization. The speed gains are almost linear when the number of transputers is increased from 4 to 64. The software is used to carry out multiple alignment of 100 sequences each of {alpha}-chain and ß-chain of hemoglobin and 83 cytochrome c sequences. The signature sequence of cytochrome c was found to be PGTKMXF. The single parameter, multiple alignment score, S, has been used to categorize proteins in different subfamilies and groups.

Received on May 29, 1992; accepted on November 10, 1992

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