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An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment(More)
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a(More)
ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases (http://www. toulouse.inra.fr/prodom.html ). ProDom-CG results from a similar domain analysis as applied to completed genomes (http://www.toulouse. inra.fr/prodomCG.html ). Recent improvements to the ProDom database and its server include:(More)
The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. The current version was built with a new improved procedure based on recursive PSI-BLAST homology searches. ProDom can be searched on the World Wide Web to study domain arrangements within either known families or new proteins, with(More)
We have developed an algorithm and a computer program for aligning new RNA sequences with a bank of aligned homologous RNA sequences. Given a common folding structure for the bank, the program performs an alignment between the bank and a new sequence, optimal both in terms of primary and secondary structure. This method is useful to align sequences that(More)
We present the outcome of a systematic analysis of protein domain shuffling in 17 completed microbial genomes. This analysis has been performed using MKDOM Version 2, a completely new version of the domain clustering program MKDOM based on PSI-BLAST recursive homology searches. It allows to delineate the most frequent protein domain building blocks, which(More)
The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. It can be searched on the World Wide Web (http://protein.toulouse.inra. fr/prodom.html ) or by E-mail (prodom@toulouse.inra.fr) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the(More)
MOTIVATION Multiple alignments of protein sequences are the basis of structural and functional analysis of protein families. It is however difficult even for an expert biologist to comprehend an alignment of more than 50 to 100 homologous sequences. RESULTS This paper presents a browser for the analysis of multiple alignments of large numbers of protein(More)
MOTIVATION To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural and functional analysis. RESULTS This paper presents an algorithm and a graphical interface called XDOM which performs a systematic analysis of the modular organization(More)
Dans ce premier article, on élabore un modèle mathématique pour décrire le mécanisme de l'induction de l'opéron lactose d'Escherichia coli. Les différentes interactions molé-culaires sont successivement représentées par des équations différentielles qui traduisent l'évolution dans le temps : des probabilités des états possibles de la région de contrôle de(More)
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