Genome Related Biological Databases

1. Genome RelatedBiological Databases

2. Content • DNA Sequence databases • Protein databases • Gene prediction • Accession numbers • NCBI website • Ensembl website

3. Nucleotide databases The underlying raw DNA sequences are identical DDBJ EMBL GenBank Housed at EBI European Bioinformatics Institute www.ebi.ac.uk/embl/ Housed in Japan www.ddbj.nig.ac.jp/Welcome-e.html Housed at NCBI National Center for Biotechnology Information www.ncbi.nlm.nih.gov/Genbank/

4. >100,000 species are represented in GenBank all species 196,538 viruses 5,214 bacteria 14,258 archaea 500 eukaryota 171,843

6. NCBI nucleotide databases • GenBank • Individual submissions • Bulk submissions (Genome centers) • High throughput sequencing (DNA) • Expressed Sequence Tags (mRNA) • RefSeq • Curated subset of GenBank • “Reference” sequence • Single sequence per locus / molecule

7. Protein databases • NCBI • RefSeq and Protein • EBI • Swiss-Prot, PIRand TrEMBL→ UniProt • Translated from nucleotide sequence • Curated • Combined

8. UniProt versusGenBank and RefSeq GenBank/RefSeq Produced by INSDC and NCBI Protein and nucleotide data Curated in RefSeq, not in GenBank UniProt Produced by SIB, EBI & Georgetown U. Protein data only Curated in SwissProt, not in TrEMBL

9. Accession numbers Label to unambiguously identify a sequence Examples (all for retinol-binding protein, RBP4): DNA X02775 GenBank genomic DNA sequence NT_030059 Genomic contig Rs7079946 dbSNP (single nucleotide polymorphism) RBP4 HUGO genenames N91759.1 An expressed sequence tag (1 of 170) NM_006744 RefSeq DNA sequence (from a transcript) NP_007635 RefSeq protein AAC02945 GenBank protein Q28369 UniProt protein 1KT7 Protein Data Bank structure record RNA protein

10. From Sequence to Genes • Gene prediction • Extrinsic • Search for genes based on observed mRNA / Protein sequences • UniGene • Ab initio • Predict genes based on genomic sequence alone • Promoter sequence • Poly(A) tail binding sites, CpG islands, splicing sites

11. UniGene • Predict genes based on ESTs • EST: • DNA sequence corresponding to mRNA from expressed gene • ~500 base pairs long • Sequenced from a cDNA library • Cluster ESTs from many cDNA libraries to predict distinct genes

12. EST clusters This is a gene with 1 EST associated; the cluster size is 1 This is a gene with 10 ESTs associated; the cluster size is 10

13. Likely to be real genes

14. Gene databases • Ensembl (EBI) • Automatic annotation: mRNA and protein sequence • Curated annotation: Vega project • Entrez Gene (NCBI) • Links RefSeq sequences to external annotations

15. Web sites for biological databases • NCBI www.ncbi.nlm.nih.gov • EBI www.ebi.ac.uk • ENSEMBL www.ensembl.org (= at EBI)

16. NCBI website

17. NCBI website

26. PubMed

27. Ensembl website

28. Ensembl structure • Gene: ENSG… • Transcript: ENST… • Protein: ENSP…

29. Ensembl search

30. OTTHUMGXXX (Curated) ENSGXXXX (Predicted)

31. Vega gene page

32. Ensembl gene page

34. Ensembl transcript page

35. Ensembl protein page