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61
The Arabidopsis information resource (TAIR): gene structure and function annotation. Nucleic Acids Research
, 2007
"... The Arabidopsis Information Resource (TAIR, ..."
doi:10.1093/nar/gkm965 The Arabidopsis Information Resource (TAIR): gene structure and function annotation
, 2007
"... The Arabidopsis Information Resource (TAIR, ..."
MIPS: analysis and annotation of proteins from whole genomes
- Nucleic Acids Res
, 2004
"... resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of.400 genomes automatically annotated w ..."
Abstract
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Cited by 206 (14 self)
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resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of.400 genomes automatically annotated
The Arabidopsis Information Resource: Impact for Identification of Important Genes in Less Known Plant Species
"... This is the second article in the series on, “Valuable Internet Resources for Plant Molecular Biology Research ” (Clark et al. 2003). In the last paper we mainly concentrated on the use of “The Arabidopsis Information Resource (TAIR) ” for obtaining basic information about genes of interest, their ..."
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This is the second article in the series on, “Valuable Internet Resources for Plant Molecular Biology Research ” (Clark et al. 2003). In the last paper we mainly concentrated on the use of “The Arabidopsis Information Resource (TAIR) ” for obtaining basic information about genes of interest
PIRSF: family classification system at the Protein Information Resource
- Nucleic Acids Res
, 2004
"... proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). PIRSF families are curated systematically based on l ..."
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Cited by 82 (13 self)
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on literature review and integrative sequence and functional analysis, including sequence and structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification and expert annotation are summarized in PIRSF family reports with graphical viewers
BIOINFORMATICS Functional Bioinformatics for Arabidopsis thaliana
"... Motivation: The genome of Arabidopsis thaliana, which has the best understood plant genome, still has approximately one third of its genes with no functional annotation at all from either MIPS or TAIR. We have applied our Data Mining Prediction (DMP) method to the problem of predicting the functiona ..."
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Motivation: The genome of Arabidopsis thaliana, which has the best understood plant genome, still has approximately one third of its genes with no functional annotation at all from either MIPS or TAIR. We have applied our Data Mining Prediction (DMP) method to the problem of predicting
Comparative and Functional Genomics Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages
, 2005
"... Abstract The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflec ..."
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used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now
DAnCER: disease-annotated chromatin epigenetics resource
- Nucleic Acids Res
, 2011
"... Chromatin modification (CM) is a set of epigenetic processes that govern many aspects of DNA repli-cation, transcription and repair. CM is carried out by groups of physically interacting proteins, and their disruption has been linked to a number of complex human diseases. CM remains largely unexplor ..."
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Cited by 2 (2 self)
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unexplored, however, especially in higher eukaryotes such as human. Here we present the DAnCER resource, which integrates information on genes with CM function from five model organisms, including human. Currently integrated are gene functional an-notations, Pfam domain architecture, protein inter
Annotating the human proteome
- Mol. Cell Proteomics
, 2005
"... The completion of the human genome has shifted the attention from deciphering the sequence to the identifica-tion and characterization of the encoded components. The identification and functional annotation of the pro-teome is here of special interest and starts with the iden-tification of genes and ..."
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Cited by 2 (0 self)
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and transcripts as a prerequisite of proteome annotation. Gene predictions are very powerful in predicting most of the exons in a genome, but reliable gene structure predictions of both known and novel genes are dependent on existing transcript and protein information. An enormous amount of data already exists
annotations using functional family assignments
, 2015
"... The widening function annotation gap in protein databases and the increasing number and diversity of the proteins being sequenced presents new chal-lenges to protein function prediction methods. Mul-tidomain proteins complicate the protein sequence– structure–function relationship further as new com ..."
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com-binations of domains can expand the functional repertoire, creating new proteins and functions. Here, we present the FunFHMMer web server, which provides Gene Ontology (GO) annotations for query protein sequences based on the functional classifi-cation of the domain-based CATH-Gene3D resource. Our
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