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| CLUSTAL-W - IMPROVING THE SENSITIVITY OF PROGRESSIVE MULTIPLE SEQUENCE ALIGNMENT THROUGH SEQUENCE WEIGHTING, POSITION-SPECIFIC GAP PENALTIES AND WEIGHT MATRIX CHOICE |
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| Author(s): THOMPSON JD, HIGGINS DG, GIBSON TJ |
| Source: NUCLEIC ACIDS RESEARCH Volume: 22 Issue: 22 Pages: 4673-4680 Published: NOV 11 1994 |
| Times Cited: 29,257 References: 39 |
| Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences, Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gap at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available. |
| Document Type: Article |
| Language: English |
Addresses:
1. EUROPEAN MOLEC BIOL LAB, D-69012 HEIDELBERG, GERMANY |
| Publisher: OXFORD UNIV PRESS UNITED KINGDOM, WALTON ST JOURNALS DEPT, OXFORD, ENGLAND OX2 6DP |
| Subject Category: Biochemistry & Molecular Biology |
| IDS Number: PU199 |
| ISSN: 0305-1048 |
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