{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T21:24:39Z","timestamp":1762032279275},"reference-count":53,"publisher":"Elsevier BV","issue":"5","license":[{"start":{"date-parts":[[2002,7,1]],"date-time":"2002-07-01T00:00:00Z","timestamp":1025481600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computers &amp; Chemistry"],"published-print":{"date-parts":[[2002,7]]},"DOI":"10.1016\/s0097-8485(02)00008-6","type":"journal-article","created":{"date-parts":[[2002,10,14]],"date-time":"2002-10-14T14:29:16Z","timestamp":1034605756000},"page":"459-477","source":"Crossref","is-referenced-by-count":46,"title":["Local weighting schemes for protein multiple sequence alignment"],"prefix":"10.1016","volume":"26","author":[{"given":"Jaap","family":"Heringa","sequence":"first","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/S0097-8485(02)00008-6_BIB1","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1006\/jmbi.1997.1287","article-title":"Do aligned sequences share the same fold?","volume":"273","author":"Abagyan","year":"1997","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB2","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1016\/0022-2836(89)90234-9","article-title":"Weights for data related by a tree","volume":"207","author":"Altschul","year":"1989","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB3","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/0022-2836(87)90226-9","article-title":"A sensitive procedure to compare amino acid sequences","volume":"193","author":"Argos","year":"1987","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB4","series-title":"Proceedings of the second international conference on Intelligent Systems for Molecular Biology","first-page":"28","article-title":"Fitting a mixture model by expectation maximisation to discover motifs in biopolymers","author":"Bailey","year":"1994"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB5","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1126\/science.257.5077.1609.b","article-title":"Response to Barton's letter: computer speed and sequence comparison","volume":"257","author":"Benner","year":"1992","journal-title":"Science"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB6","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0097-8485(96)80003-9","article-title":"A flexible motif search technique based on generalized profiles","volume":"20","author":"Bucher","year":"1996","journal-title":"Comput. Chem."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB7","series-title":"Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology (ISMB)","first-page":"44","article-title":"A sequence similarity approach based on a probabilistic interpretation of an alignment scoring system","author":"Bucher","year":"1996"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB8","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1137\/0148063","article-title":"The multiple sequence alignment problem in biology","volume":"48","author":"Carillo","year":"1988","journal-title":"SIAM J. Appl. Math."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB9","unstructured":"Dayhoff, M.O. 1978. Atlas of Protein Structure and Sequence, National Biomedical Research Foundation, Washington DC, USA, 4, Suppl. 3."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB10","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB11","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1007\/BF02603120","article-title":"Progressive sequence alignment as a prerequisite to correct phylogenetic trees","volume":"25","author":"Feng","year":"1987","journal-title":"J. Mol. Evol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB12","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/0022-2836(82)90398-9","article-title":"An improved algorithm for matching biological sequences","volume":"162","author":"Gotoh","year":"1982","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB13","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1126\/science.1604319","article-title":"Exhaustive matching of the entire protein sequence database","volume":"256","author":"Gonnet","year":"1992","journal-title":"Science"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB14","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1006\/jmbi.1996.0679","article-title":"Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments","volume":"264","author":"Gotoh","year":"1996","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB15","doi-asserted-by":"crossref","first-page":"4355","DOI":"10.1073\/pnas.84.13.4355","article-title":"Profile analysis: detection of distantly related proteins","volume":"84","author":"Gribskov","year":"1987","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB16","doi-asserted-by":"crossref","first-page":"10\u2008915","DOI":"10.1073\/pnas.89.22.10915","article-title":"Amino acid substitution matrices from protein blocks","volume":"89","author":"Henikoff","year":"1992","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB17","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1016\/0022-2836(94)90032-9","article-title":"Position-based sequence weights","volume":"243","author":"Henikoff","year":"1994","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB18","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1016\/S0959-440X(97)80060-7","article-title":"Three-dimensional domain duplication, swapping and stealing","volume":"7","author":"Heringa","year":"1997","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB19","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/S0959-440X(98)80068-7","article-title":"Detection of internal repeats: how common are they?","volume":"8","author":"Heringa","year":"1998","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB20","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/S0097-8485(99)00012-1","article-title":"Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment","volume":"23","author":"Heringa","year":"1999","journal-title":"Comput. Chem."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB21","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/BF02257378","article-title":"The alignment of sets of sequences and the construction of phylogenetic trees. An integrated method","volume":"20","author":"Hogeweg","year":"1984","journal-title":"J. Mol. Evol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB22","first-page":"373","article-title":"A space-efficient algorithm for local similarities","volume":"6","author":"Huang","year":"1990","journal-title":"CABIOS"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB23","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/0196-8858(91)90017-D","article-title":"A time-efficient, linear-space local similarity algorithm","volume":"12","author":"Huang","year":"1991","journal-title":"Adv. Appl. Math."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB24","doi-asserted-by":"crossref","first-page":"2264","DOI":"10.1073\/pnas.87.6.2264","article-title":"Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes","volume":"87","author":"Karlin","year":"1990","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB25","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1093\/bioinformatics\/14.10.846","article-title":"Hidden markov models for detecting remote protein homologies","volume":"14","author":"Karplus","year":"1998","journal-title":"Bioinformatics"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB26","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1126\/science.8211139","article-title":"Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment","volume":"262","author":"Lawrence","year":"1993","journal-title":"Science"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB27","doi-asserted-by":"crossref","first-page":"4412","DOI":"10.1073\/pnas.86.12.4412","article-title":"A tool for multiple sequence alignment","volume":"86","author":"Lipman","year":"1989","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB28","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1002\/pro.5560030118","article-title":"Improving the sensitivity of the sequence profile method","volume":"3","author":"L\u00fcthy","year":"1994","journal-title":"Protein Sci."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB29","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1093\/bioinformatics\/15.3.211","article-title":"DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment","volume":"15","author":"Morgenstern","year":"1999","journal-title":"Bioinformatics"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB30","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the amino acid sequence of two proteins","volume":"48","author":"Needleman","year":"1970","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB31","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1093\/nar\/24.8.1515","article-title":"SAGA: sequence alignment by genetic algorithm","volume":"24","author":"Notredame","year":"1996","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB32","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: a novel method for fast and accurate multiple sequence alignment","volume":"302","author":"Notredame","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0022-2836(89)90084-3","article-title":"Protein structure alignment","volume":"208","author":"Taylor","year":"1989","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB34","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1093\/protein\/5.2.121","article-title":"A data bank merging related protein structures and sequences","volume":"5","author":"Pascarella","year":"1992","journal-title":"Protein Eng."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB35","doi-asserted-by":"crossref","first-page":"3836","DOI":"10.1093\/nar\/24.19.3836","article-title":"Searching databases of conserved sequence regions by aligning protein multiple-alignments","volume":"24","author":"Pietroskovski","year":"1996","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB36","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1093\/protein\/12.2.85","article-title":"Twilight zone of protein sequence alignment","volume":"12","author":"Rost","year":"1999","journal-title":"Protein Eng."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB37","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB38","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1002\/prot.340090107","article-title":"Database of homology derived protein structures and the structural meaning of sequence alignment","volume":"9","author":"Sander","year":"1991","journal-title":"Proteins"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB39","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1016\/S0022-2836(99)80003-5","article-title":"Weighting aligned protein or nucleic acid sequences to correct for unequal representation","volume":"216","author":"Sibbald","year":"1990","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB40","first-page":"327","article-title":"Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology","volume":"12","author":"Sj\u00f6lander","year":"1996","journal-title":"Comp. Appl. Biosci."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB41","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","article-title":"Identification of common molecular subsequences","volume":"147","author":"Smith","year":"1981","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB42","first-page":"625","article-title":"DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment","volume":"13","author":"Stoye","year":"1997","journal-title":"Comput. Appl. Biosci."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB43","doi-asserted-by":"crossref","unstructured":"Sunyaev, S.R., Rodchenkov, I.V., Eisenhaber, F., Kuznetsov, E.N. 1998. Analysis of the position dependent amino acid probabilities and its application to the search for remote homologues. In: Proceedings of the 2nd Annual International Conference on Computers in Molecular Biology (RECOMB98), pp. 258\u2013264.","DOI":"10.1145\/279069.279127"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB44","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1093\/protein\/12.5.387","article-title":"PSIC: profile extraction from sequence alignments with position-specific counts of independent observations","volume":"12","author":"Sunyaev","year":"1999","journal-title":"Protein Eng."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB45","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/BF02143508","article-title":"A flexible method to align large numbers of biological sequences","volume":"28","author":"Taylor","year":"1988","journal-title":"J. Mol. Evol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB46","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB47","doi-asserted-by":"crossref","first-page":"2682","DOI":"10.1093\/nar\/27.13.2682","article-title":"A comprehensive comparison of multiple sequence alignment programs","volume":"27","author":"Thompson","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB48","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1093\/bioinformatics\/15.1.87","article-title":"BAliBASE: a benchmark alignment database for the evaluation of multiple sequence alignment programs","volume":"15","author":"Thompson","year":"1999","journal-title":"Bioinformatics"},{"key":"10.1016\/S0097-8485(02)00008-6_BIB49","first-page":"115","article-title":"A fast and sensitive multiple sequence alignment program","volume":"5","author":"Vingron","year":"1989","journal-title":"Comp. Appl. Biosci."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB50","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1006\/jmbi.1995.0340","article-title":"An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited","volume":"249","author":"Vogt","year":"1995","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB51","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1089\/cmb.1994.1.337","article-title":"On the complexity of multiple sequence alignment","volume":"1","author":"Wang","year":"1994","journal-title":"J. Comput. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB52","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/0022-2836(87)90478-5","article-title":"A new algorithm for best subsequences alignment with applications to the tRNA-rRNA comparisons","volume":"197","author":"Waterman","year":"1987","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0097-8485(02)00008-6_BIB53","series-title":"Bioinformatics: Sequences, structure and databanks, Practical Approach Series","article-title":"Comparison of protein sequences and practical database searching","author":"Yona","year":"2000"}],"container-title":["Computers &amp; Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0097848502000086?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0097848502000086?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T16:26:58Z","timestamp":1680712018000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0097848502000086"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2002,7]]},"references-count":53,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2002,7]]}},"alternative-id":["S0097848502000086"],"URL":"https:\/\/doi.org\/10.1016\/s0097-8485(02)00008-6","relation":{},"ISSN":["0097-8485"],"issn-type":[{"value":"0097-8485","type":"print"}],"subject":[],"published":{"date-parts":[[2002,7]]}}}