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2004

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Animals

Royal College of Surgeons in Ireland

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Full-Text Articles in Life Sciences

Gasp: Gapped Ancestral Sequence Prediction For Proteins., Richard J. Edwards, Denis C. Shields Sep 2004

Gasp: Gapped Ancestral Sequence Prediction For Proteins., Richard J. Edwards, Denis C. Shields

Molecular and Cellular Therapeutics Articles

BACKGROUND: The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments.

RESULTS: Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first ...