Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability

Details

Serval ID
serval:BIB_70CBBA16D432
Type
Article: article from journal or magazin.
Collection
Publications
Title
Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability
Journal
Computer Applications in the Biosciences
Author(s)
Depiereux  E., Baudoux  G., Briffeuil  P., Reginster  I., De Bolle  X., Vinals  C., Feytmans  E.
ISSN
0266-7061 (Print)
Publication state
Published
Issued date
06/1997
Volume
13
Number
3
Pages
249-56
Notes
Journal Article
Research Support, Non-U.S. Gov't --- Old month value: Jun
Abstract
MOTIVATION: The Match-Box software comprises protein sequence alignment tools based on strict statistical thresholds of similarity between protein segments. The method circumvents the gap penalty requirement: gaps being the result of the alignment and not a governing parameter of the procedure. The reliable conserved regions outlined by Match-Box are particularly relevant for homology modelling of protein structures, prediction of essential residues for site-directed mutagenesis and oligonucleotide design for cloning homologous genes by polymerase chain reaction (PCR). RESULTS: The method produces reliable results, as assessed by tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation to a threshold of similarity progressively raised to extend the aligned regions to their maximal length, up to the significance limit of matching segments. The score obtained at each position is printed below the sequences and allows a discriminant reading of each aligned region. AVAILABILITY: Sequences may be submitted to a Web server at http://www.fundp.ac.be/sciences/biologie/bms/+ ++matchbox_submit.html or sent by e-mail to matchbox/biq.fundp.ac.be (help available by just mailing help).
Keywords
Algorithms Amino Acid Sequence Animals Aspartic Endopeptidases/genetics Conserved Sequence Humans Molecular Sequence Data Proteins/*genetics Reproducibility of Results Sequence Alignment/*methods/statistics & numerical data Sequence Homology, Amino Acid *Software
Pubmed
Web of science
Create date
28/01/2008 11:03
Last modification date
20/08/2019 14:29
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