Gene-centered resources at NCBI

Transcription

1 COURSE OF BIOINFORMATICS a.a Gene-centered resources at NCBI

2 We searched Accession Number: M60495 AT NCBI Nucleotide

3 Gene has been implemented at NCBI to organize information about genes, serving as a major node in the nexus of genomic map, sequence, expression, protein structure, function, and homology data.

4 Each Gene record is assigned a unique identifier, the GeneID The content of a Gene record is organized in: Nomenclature (official symbol, full name, Alias, ) Summary (quick synopsys of gene function) Map Data (Genomic content, Genomic region, ) Sequence-related data (gene, genome, transcript and protein RefSeq) Function (bibliography, GeneRIF, GO, pathways) Variation (dbsnps) Homology (related genes in other species, ) Other sites (links to external databases)

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14 NCBI s Reference Sequence (RefSeq) database is a collection of taxonomically diverse, non- redundant and richly annotated sequences representing naturally occurring molecules of DNA, RNA, and protein.

15 International Nucleotide Sequence Database Collaboration (INSDC) Figure 2. RefSeq Processing Pipelines. Sequence data deposited in the public archival databases is available for RefSeq processing. Processing pipelines include the vertebrate curation pipeline, the computational genome annotation pipeline, and extraction from GenBank. These pipelines generate new and updated RefSeq records that become publicly available in Entrez Nucleotide, Protein, and Gene databases. (A) Once a gene is defined and associated with sufficient sequence information in an Internal curation database, it can be pushed into the RefSeq pipeline. The RefSeq process is initiated by selecting the Longest mrna annotated with a complete coding sequence for each locus. This RefSeq record has a status of PROVISIONAL, PREDICTED, or INFERRED. Subsequent curation may result in a sequence or annotation update and a RefSeq status of VALIDATED or REVIEWED. Records are updated if the underlying INSDC submission is updated or I f other associated data are updated, including nomenclature, publications, or map location. (B) Available RefSeq and INSDC data are aligned to an assembled genome, ab initio gene prediction that uses the alignment data is performed, and an analysis program integrates all available data to define the annotation models. New MODEL RefSeq records are generated by this pipeline. (C) When a complete, annotated genome becomes available in the INSDC, a set of corresponding RefSeq records are generated by duplicating the GenBank records, followed by validation and addition of cross-references to Gene (via a db_xref citing the GeneID) and more informative and standardized protein names, when available.

16 Search the NUCLEOTIDE database for: NM_ and NG_ Which differences do you note in annotations? Search them in the GENE database

17 Click on GRAPHICS

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20 How to query GENE By chromosomal region By RefSeq status By Taxonomy Et al.

21 Other Gene-centered databses at NCBI

22 Homologene

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24 Gene Expression Omnibus (GEO) GEO Profiles

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27 Online Mendelian Inheritance in Man OMIM

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29 MIM number prefix translation * # + % An asterisk indicates a gene of known sequence. A number symbol indicates that it is a descriptive entry, usually of a phenotype. The reason for the use of the # sign is given in the first paragraph of the entry. Discussion of any gene(s) related to the phenotype resides in another entry(ies) as described in the first paragraph. A plus sign indicates that the entry contains the description of a gene of known sequence and a phenotype. A percent sign indicates that the entry describes a confirmed mendelian phenotype or phenotypic locus for which the underlying molecular basis is not known. No symbol generally indicates a description of a phenotype for which the mendelian basis, although suspected, has not been clearly established or that the separateness of this phenotype from that in another entry is unclear.

30 Exercise: Find GeneID:546 Which gene it correspond to? What about gene annotation

31 Where to study