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 gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
Keywords
BiologySequence (biology)Position (finance)WeightingMultiple sequence alignmentSensitivity (control systems)Sequence alignmentMatrix (chemical analysis)GeneticsComputational biologyPeptide sequenceGene
Affiliated Institutions
Related Publications
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system...
MAFFT version 5: improvement in accuracy of multiple sequence alignment
The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i...
DCSE, an interactive tool for sequence alignment and secondary structure research
DCSE provides a user-friendly package for the creation and editing of sequence alignments. The program runs on different platforms, including microcomputers and workstations. Ap...
Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.
We describe an approach to analyzing protein sequence databases that, starting from a single uncharacterized sequence or group of related sequences, generates blocks of conserve...
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
We define a “threaded blockset,” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner...
Publication Info
- Year
- 1994
- Type
- article
- Volume
- 22
- Issue
- 22
- Pages
- 4673-4680
- Citations
- 64103
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
64103
OpenAlex
Cite This
Julie Thompson,
Desmond G. Higgins,
Toby J. Gibson
(1994).
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Research
, 22
(22)
, 4673-4680.
https://doi.org/10.1093/nar/22.22.4673
Identifiers
- DOI
- 10.1093/nar/22.22.4673