E. L. Sonnhammer and D. Kahn. The Modular Arrangement of Proteins as Inferred from Analysis of Homology. Protein Science, 3:482--492, 1994.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....des programmes similaires Fasta [11] 13] ou Blast [1] optimises pour des machines sequentielles : a temps de calcul comparables, les resultats des machines paralleles semblent de meilleure qualite. Cependant, certains traitements relatifs a l analyse ou la structuration de banques entieres [17] conduisent, meme en utilisant ces machines, ades temps de calcul gigantesques. A titre d exemple, l extraction de sous sequences homologues, c est adire de portion de sequences similaire, dans une banque de 20 000 sequences proteiques (Swiss Prot 21, par exemple) demande approximativement ....

....cas, le centre serveur dispose d une ou plusieurs machines specialisees qu il active en fonction des requetes. L autre secteur d utilisation concerne l usage intensif de telles machines. Les recherches menees, par exemple, sur la classification d une banque de sequences par analyse d homologies [17] demandent une masse de calculs gigantesque. Dans ce cas, l exploitation permanente (ou sur un temps tres long) d une ressource d un centre serveur n est pas envisageable. Le faible cout d une machine specialisee (comparativement a une machine parallele programmable qui o#rirait les memes ....

E. L. Sonnhammer and D. Kahn. The Modular Arrangement of Proteins as Inferred from Analysis of Homology. Protein Science, 3:482--492, 1994.

....domains, motifs or patterns. Some examples include the SBASE protein domain library [Pongor et al. 1994] the BLOCKS database of aligned sequence segments [Henikoff Henikoff, 1991] the PRINTS database of protein motif fingerprints [Attwood et al. 1994] and the ProDom protein domain database [Sonnhammer Kahn, 1994]. While several domain motif databases are being compiled, it is important to develop database search methods that fully utilize the conserved structural and functional information embedded in those databases to enhance search sensitivity. In this paper we report a new method, termed MOTIFIND ....

Sonnhammer, E. L. L. & Kahn, D. (1994) Modular arrangement of proteins as inferred from analysis of homology. Prot. Sci., 3, 482-492.

....a query sequence, and we want to know which ones of a set of multialignments are similar to the query. This approach has a direct application with the database ProDom. We applied our method to the ProDom28 version, which contains ungapped alignments. 4.2. 1 Overview of ProDom28 database ProDom28 [19] has been generated from SWISSPROT28 4 as follows: ffl pairwise comparisons of SWISSPROT sequences produce a set of HSPs (High Scoring Segment Pairs) ffl from overlapping HSPs are built bigger HSSs (High Scoring Segment Sets) and a graph of HSSs; ffl multiple alignments are produced by ....

Sonnhamer, E. L., and Kahn, D. The modular arrangement of proteins as inferred from analysis of homology. Protein Science 3 (1994), 482--492.

....which pattern they have. It does not have the problem on multidomain proteins. It piles up the regional similarities among protein sequences into statistically signi#cant character patterns and then classify the sequences with their patterns into groups, which are not necessarily disjoint sets [24, 26]. Thus multidomain proteins can be classi#ed into two or more di#erent groups simultaneously. However, since the length of the patterns and the degree of their conservation vary depending on sequence groups, it is di#cult to detect the su#cient number of patterns and to evaluate their statistical ....

....their statistical signi#cance for classifying protein sequences. H. Matsuda et al. Theoretical Computer Science 210 (1999) 305 325 307 For this reason, current implementations of this approach usually limit the initial stage of pattern detection to #xed length ungapped sequence comparison [24, 26]. This limitation may reduce sensitivity of pattern detection and some distantly related sequences may not be classi#ed in a group. To cope with these issues, we propose a method for classifying whole genome protein sequences on the basis of the similarity based approach. The goal of our method ....

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E.L.L. Sonnhammer, D. Kahn, Modular arrangement of proteins as inferred from analysis of homology, Protein Sci. 3 (1994) 482-- 492.

....( domains ) could be used to discriminate among functions. Although using a multiple sequence alignment to identify di erences at the level of individual amino acids might be desirable, there are far too many di erences at this level of description for e ective induction. The ProDom database [13] is one attempt to systematically de ne protein domains, done on the basis of local sequence alignments within a large set of sequences. We used our visualization tools to explore it and other possible domain de nitions (e.g. P Fam, 12] We judged the larger number of ProDom domains per protein, ....

E. Sonnhammer and D. Kahn. The modular arrangement of proteins as inferred from analysis of homology. Protein Science, 3:482-489, 1994. 14

....containing these patterns. Some examples of the use of these representations in searching protein data bases include [33, 79, 80] Statistical characterizations of sequence and structural motifs include Helix Turn Helix [49] the calcium binding EF hand [47] and libraries of motifs such as [9, 39, 70]. Statistical representations of patterns in nucleic acids have been used to characterize and search for regulatory regions in DNA (see, for example, 17, 26, 28, 72] MSA s are also used to identify subsequences for laboratory techniques, such as PCR and library screening, that isolate DNA ....

E. L. Sonnhammer and D. Kahn. Modular arrangement of proteins as inferred from analysis of homology. Protein Science, 3:482--492, 1994.

....meaningful partitioning of the data. Neither do we attempt to delineate domains. The domain structure of proteins is, of course, the main obstacle to the application of traditional clustering procedures like single linkage clusterings. This is the motivation for algorithms like DOMAINER [18] or the graph theoretical clustering algorithm of [10] In contrast to these methods ours attempts only to cluster together sequences that share global, or at least very strong, similarity. It does so while at the same time maintaining a clear distinction between different clusters. It is based ....

Sonnhammer, E.L.L. and Kahn, D., "Modular arrangement of proteins as inferred from analysis of homology", Protein Science, 3:482-492, 1994.

....in view of the large number of newly sequenced proteins which await analysis. Generally, the existing approaches can be divided into those based on short conserved motifs (e.g. Bairoch et al. 1997, Attwood et al. 1998, Henikoff Henikoff 1991] and those which are based on whole domains (e.g. [Sonnhammer Kahn 1994, Sonnhammer et al. 1997] The manually defined patterns in PROSITE have served as an excellent seed for several such works. The methods used to represent these motifs and domains vary, and among the most popular forms are the consensus patterns [Bairoch et al. 1997, Attwood et al. 1998] the ....

Sonnhammer, E. L. L. & Kahn, D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3, 482-492.

....in view of the large number of newly sequenced proteins which await analysis. Generally, the existing approaches can be divided into those based on short conserved motifs (e.g. Bairoch et al. 1997, Attwood et al. 1998, Heniko Heniko 1991] and those which are based on whole domains (e.g. [Sonnhammer Kahn 1994, Sonnhammer et al. 1998] The manually de ned patterns in PROSITE have served as an excellent seed for several such works. The methods used to represent these motifs and domains vary, and among the most popular forms are the consensus patterns [Bairoch et al. 1997, Attwood et al. 1998] the ....

Sonnhammer, E. L. L. & Kahn, D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3, 482-492.

....39 3.1 Motif and domain based analyses . 39 3.1.1 The PROSITE dictionary [Bairoch 1991] 39 3.1.2 The BLOCKS database [Henikoff Henikoff 1991] 40 3.1. 3 The ProDom database[Sonnhammer Kahn 1994] . 40 3.1.4 The Pfam database [Sonnhammer et al. 1997] 41 3.1.5 The DOMO database [Gracy Argos 1998] 41 3.2 Protein based analysis . ....

....analyses Most of these studies yielded databases of protein motifs and domains. Such databases have become an important tool for the analysis of newly discovered protein sequences. Among these are PROSITE [Bairoch 1991] Blocks [Henikoff Henikoff 1991] PRINTS [Attwood Beck 1994] ProDom [Sonnhammer Kahn 1994], Pfam [Sonnhammer et al. 1997] and Domo [Gracy Argos 1998] The manually defined patterns in PROSITE have served as an excellent seed for several such studies. These studies differ from each other in several aspects. Some are based on manual or semimanual procedures (e.g. PROSITE, PRINTS) ....

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Sonnhammer, E. L. L. & Kahn, D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3, 482-492.

....Hidden Markov Models for Multiple Sequence Alignment William N. Grundy . Charles P. Elkan Dept. of Computer Science Engineering University of California, San Diego Abstract . Protein families are well characterized by a collection of motifs (Sonnhammer Kahn 1994), sometimes referred to as the common core (Chothia Lesk 1986) These motifs can have structural and functional significance, and they may frequently be operated upon as units by diverse evolutionary mechanisms. The quality of a multiple alignment depends upon how accurately it ....

Sonnhammer, E. and D. Kahn. "The modular arrangement of proteins as inferred from analysis of homology." Protein Science, 3:482492, 1994.

....number of sequences [Gribskov et al. 1987, Taylor 1990] Only few computational studies considered all, or many, of the known sequences. These studies focus on (i) searching for motifs, signature sequences and domains [Henikoff Henikoff 1991, Sheridan Venkataraghavan 1992, Harris et al. 1992, Sonnhammer Kahn 1994, Han Baker 1995, Hanke et al. 1996] ii) improving mutation matrices [Gonnet et al. 1992, Henikoff Henikoff 1992] iii) automatic classification of protein sequences into families [Wu et al. 1992, Ferran et al. 1994] iv) extraction of similarity relationships between protein sequences ....

Sonnhammer, E. L. L. & Kahn, D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Protein Science 3, 482-492.

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Sonnhammer, E L L & Kahn, D (1994) Modular arrangement of proteins as inferred from analysis of homology. Protein Science 3, 482-492.

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Sonnhammer, E.L.L., Kahn, D. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3:482--492, 1994.

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