Publications (2)10.48 Total impact
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Article: Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names
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ABSTRACT: There is no control over the information provided with sequences when they are deposited in the sequence databases. Consequently mistakes can seed the incorrect annotation of other sequences. Grouping genes into families and applying controlled annotation overcomes the problems of incorrect annotation associated with individual sequences. Two databases (http://www.mendel.ac.uk) were created to apply controlled annotation to plant genes and plant ESTs: Mendel-GFDb is a database of plant protein (gene) families based on gapped-BLAST analysis of all sequences in the SWISS-PROT family of databases. Sequences are aligned (ClustalW) and identical and similar residues shaded. The families are visually curated to ensure that one or more criteria, for example overall relatedness and/or domain similarity relate all sequences within a family. Sequence families are assigned a ‘Gene Family Number’ and a unified description is developed which best describes the family and its members. If authority exists the gene family is assigned a ‘Gene Family Name’. This information is placed in Mendel-GFDb. Mendel-ESTS is primarily a database of plant ESTs, which have been compared to Mendel-GFDb, completely sequenced genomes and domain databases. This approach associated ESTs with individual sequences and the controlled annotation of gene families and protein domains; the information being placed in Mendel-ESTS. The controlled annotation applied to genes and ESTs provides a basis from which a plant transcription database can be developed.Nucleic Acids Research 02/2001; · 8.03 Impact Factor -
Article: Mendel-ESTS: Database of Plant ESTs in dbEST Annotated with Gene Family Numbers and Gene Family Names
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ABSTRACT: The rapid expansion of gene sequencing has led to an exponential increase in the number of genes being deposited in the sequence databases. Associated with this is the proliferation of idiosyncratic gene names. The DE field descriptions in closely related sequences, whether they be from the same or different species, particularly in the EMBL and TrEMBL databases are often inconsistent and sometimes incorrect and misleading (Galperin and Koonin 1998). In an attempt to unify gene nomenclature and DE field descriptions, initially within the plants, two databases have been created: Mendel-GFDb (genes arranged into gene families) and Mendel-ESTS (plant EST and STS sequences related to genes in Mendel-GFDb by gene family numbers). The database web addresses are:Mendel-GFDb and Mendel-ESTS: http://www.mendel.ac.uk/US Mirror: http://genome.cornell.edu/Plant Molecular Biology Reporter 08/1999; 17(3):239-247. · 2.45 Impact Factor
