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134
MIPS: a database for genomes and protein sequences
- Nucleic Acids Res
, 2002
"... The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually a ..."
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Cited by 336 (10 self)
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annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB
STRING 7–recent developments in the integration and prediction of protein interactions
- Nucleic Acids Res
, 2007
"... Information on protein–protein interactions is still mostly limited to a small number of model organisms, and originates from a wide variety of experimental and computational techniques. The database and online resource STRING generalizes access to protein interaction data, by integrating known and ..."
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Cited by 125 (13 self)
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and predicted interactions from a variety of sources. The underlying infrastructure includes a consistent body of completely sequenced genomes and exhaustive orthology classifications, based on which interaction evidence is transferred between organisms. Although primarily developed for protein interaction
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes
, 2001
"... The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes (http:// www.ebi.ac.uk/proteome/). The two main projects used ..."
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Cited by 24 (11 self)
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used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31--67% (InterPro statistics) of the proteins from each of the complete genomes. CluSTr covers the three complete eukaryotic genomes and the incomplete human genome data. The Proteome Analysis Database
The PIR-International Protein Sequence Database
, 1999
"... The Protein Information Resource (PIR; http://wwwnbrf. georgetown.edu/pir/ ) supports research on molecular evolution, functional genomics, and computational biology by maintaining a comprehensive, non-redundant, well-organized and freely available protein sequence database. Since 1988 the database ..."
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Cited by 56 (1 self)
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has been maintained collaboratively by PIR-International, an international association of data collection centers cooperating to develop this resource during a period of explosive growth in new sequence data and new computer technologies. The PIR Protein Sequence Database entries are classified
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.
- Nature Methods,
, 2009
"... Articles nAture methods | VOL.6 NO.9 | september 2009 | 673 metagenomics projects collect dnA from uncharacterized environments that may contain thousands of species per sample. one main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups represent ..."
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Cited by 57 (3 self)
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Articles nAture methods | VOL.6 NO.9 | september 2009 | 673 metagenomics projects collect dnA from uncharacterized environments that may contain thousands of species per sample. one main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups
Phylogenomic inference of protein molecular function: advances and challenges
- Bioinformatics
, 2004
"... Motivation: Protein families evolve a multiplicity of functions through gene duplication, speciation and other processes. As a number of studies have shown, standard methods of protein function prediction produce systematic errors on these data. Phylogenomic analysis—combining phylogenetic tree cons ..."
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Cited by 76 (3 self)
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and fundamental principles of phylogenomic analysis, new methods developed for the key tasks, benchmark datasets for these tasks (when available) and suggest procedures to increase accuracy. We also discuss some of the methods used in the Celera Genomics high-throughput phylogenomic classification of the human
HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res
, 1994
"... Comparison of homologous genes is a major step for many studies related to genome structure, function or evolution. Similarity search programs easily find genes homologous to a given sequence. However, only very tedious manual procedures allow the retrieval of all sets of homologous genes sequenced ..."
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Cited by 55 (7 self)
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corresponds to GenBank sequences from all vertebrate species, with some data corrected, clarified, or completed, notably to address the problem of redundancy. Coding sequences have been classified in gene families. Protein multiple alignments and phylogenetic trees have been calculated for each family
Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases
, 2010
"... LRR-kinases constitute the largest subfamily of receptor-like kinases in plants and regulate a wide variety of processes related to development and defense. Through a reiterative process of sequence analysis and re-annotation, we identified 309 LRR-kinase genes in the rice genome (Nipponbare). Among ..."
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Cited by 9 (0 self)
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). Among them, 127 genes in the Rice Annotation Project Database and 85 in Refseq of NCBI were amended (in addition, 62 LRR-kinase genes were not annotated in Refseq). The complete set of LRR-kinases was characterized. These LRR-kinases were classified into five groups according to phylogenetic analysis
Predicting protein function with hierarchical phylogenetic profiles: the Gene3D PhyloTuner method applied to eukaryotic genomes
- PLoS Comput. Biol
, 2007
"... ‘‘Phylogenetic profiling’ ’ is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited or eliminated in a codependent manner. Creating presence–absence profiles of orthologous genes is now a common and powerful way of identifying function ..."
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Cited by 12 (4 self)
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. Using CATH structural domain assignments from the Gene3D database for 13 complete eukaryotic genomes, we have developed a novel modification of the phylogenetic profiling method that uses genome copy number of each domain superfamily to predict functional relationships. In our approach, superfamilies
A Framework for Classification of Prokaryotic Protein
"... Background: Overwhelming majority of the Serine/Threonine protein kinases identified by gleaning archaeal and eubacterial genomes could not be classified into any of the well known Hanks and Hunter subfamilies of protein kinases. This is owing to the development of Hanks and Hunter classification sc ..."
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Cited by 3 (0 self)
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scheme based on eukaryotic protein kinases which are highly divergent from their prokaryotic homologues. A large dataset of prokaryotic Serine/Threonine protein kinases recognized from genomes of prokaryotes have been used to develop a classification framework for prokaryotic Ser/Thr protein kinases
Results 1 - 10
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