Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment.

J Heringa

doi:10.1016/s0097-8485(99)00012-1

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Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment.

J Heringa

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Abstract

Multiple sequence alignment remains one of the most powerful tools for assessing sequence relateness and the identification of structurally and functionally important protein regions. In this work, two new techniques are introduced to increase the sensitivity of dynamic programming and to enable checks for alignment consistency: Profile-preprocessed and secondary structure-induced alignments. Both strategies are based upon the hierarchical dynamic programming technique and can be applied separately or used in combination. Alignments resulting from the strategies are shown in comparison with the multiple alignment methods CLUSTALX and MULTAL for distant sequence sets of the flavoxin and cupredoxin protein families.

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Amino Acid Sequence Cluster Analysis Database Management Systems Molecular Sequence Data Protein Structure, Secondary Sequence Alignment Sequence Homology, Amino Acid Journal Article

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J Heringa. 1999-06-15. Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment.. https://doi.org/10.1016/s0097-8485(99)00012-1

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