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© Oxford University Press

An algorithm to determine protein sequence alignment by utilizing data obtained from a peptide mixture and individual peptides

Carlo Caporale 1,*, Ciro Sepe 1, Carla Caruso 1, Pasquale Petrilli 2 and Vincenzo Buonocore 1

1Dipartimento di Agrobiologia ed Agrochimica, Universita' delta Tuscia via S.Camillo de Lellis, 01100, Viterbo, Italy
2Istituto di Industrie Agrarie, Universita' di Napoli Portici, Italy

*To whom reprints requests should be sent

With the aim of limiting peptide purification steps and unambiguously ascertaining protein sequences, we have designed and implemented on a personal computer an algorithm to determine sequence alignment by utilizing data obtained from automatic Edman degradation performed on a single peptide mixture and individual peptides. The protein under study is digested by two different hydrolysis methods and fragments are just isolated from one mixture and sequenced, while the second mixture is submitted unfractionated to sequence analysis. The algorithm provides for the exact alignment of the individual peptides using the mixture data for the overlapping. We report an example of application of this approach by utilizing experimental data obtained from a protein of known sequence.

Received on February 26, 1994; accepted on July 21, 1994

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