Multiple alignment of sequences on parallel computers

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 beta-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.

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