Similarity Query
Mostrando 25-36 de 60 artigos, teses e dissertações.
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25. Protein ranking: From local to global structure in the protein similarity network
Biologists regularly search databases of DNA or protein sequences for evolutionary or functional relationships to a given query sequence. We describe a ranking algorithm that exploits the entire network structure of similarity relationships among proteins in a sequence database by performing a diffusion operation on a precomputed, weighted network. The resul
National Academy of Sciences.
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26. Integrated databanks access and sequence/structure analysis services at the PBIL
The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our
Oxford University Press.
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27. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale
The combination of sequencing and post-sequencing experimental approaches produces huge collections of data that are highly heterogeneous both in structure and in semantics. We propose a new strategy for the integration of such data. This strategy uses structured sets of sequences as a unified representation of biological information and defines a probabilis
Oxford University Press.
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28. PowerBLAST: A New Network BLAST Application for Interactive or Automated Sequence Analysis and Annotation
As the rate of DNA sequencing increases, analysis by sequence similarity search will need to become much more efficient in terms of sensitivity, specificity, automation potential, and consistency in annotation. PowerBLAST was developed, in part, to address these problems. PowerBLAST includes a number of options for masking repetitive elements and low complex
Cold Spring Harbor Laboratory Press.
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29. BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available. However, with the increasingly large da
Oxford University Press.
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30. Recent changes in the GenBank On-line Service.
The GenBank On-line Service provides access to the GenBank and EMBL nucleic acid sequence databases and to the Swiss-Prot and GenPept protein sequence databases. Users can query the databases by sequence similarity and annotation keywords and retrieve entries of interest. This access is available through e-mail servers, anonymous FTP, anonymous interactive l
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31. CDART: Protein Homology by Domain Architecture
The Conserved Domain Architecture Retrieval Tool (CDART) performs similarity searches of the NCBI Entrez Protein Database based on domain architecture, defined as the sequential order of conserved domains in proteins. The algorithm finds protein similarities across significant evolutionary distances using sensitive protein domain profiles rather than by dire
Cold Spring Harbor Laboratory Press.
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32. NEMBASE: a resource for parasitic nematode ESTs
NEMBASE (available at http://www.nematodes.org) is a publicly available online database providing access to the sequence and associated meta-data currently being generated as part of the Edinburgh–Wellcome Trust Sanger Institute parasitic nematode EST project. NEMBASE currently holds ∼100 000 sequences from 10 different species of nematode. To facilitate
Oxford University Press.
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33. PathBLAST: a tool for alignment of protein interaction networks
PathBLAST is a network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. The basic method searches for high-scoring alignments between pairs of protein interaction paths, for which proteins of the first path are paired with putative orthologs o
Oxford University Press.
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34. The sperm outer dense fiber protein is the 10th member of the superfamily of mammalian small stress proteins
Nine proteins have been assigned to date to the superfamily of mammalian small heat shock proteins (sHsps): Hsp27 (HspB1, Hsp25), myotonic dystrophy protein kinase–binding protein (MKBP) (HspB2), HspB3, αA-crystallin (HspB4), αB-crystallin (HspB5), Hsp20 (p20, HspB6), cardiovascular heat shock protein (cvHsp [HspB7]), Hsp22 (HspB8), and HspB9. The most p
Cell Stress Society International.
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35. Protein sequence similarity searches using patterns as seeds.
Protein families often are characterized by conserved sequence patterns or motifs. A researcher frequently wishes to evaluate the significance of a specific pattern within a protein, or to exploit knowledge of known motifs to aid the recognition of greatly diverged but homologous family members. To assist in these efforts, the pattern-hit initiated BLAST (PH
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36. The ProDom database of protein domain families.
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 ([email protected]) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the g