1. Introduction to Genes and Genomes with Ensembl

2. Large amounts of raw DNA sequence data
CGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAAC ACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCT GGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGC CACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTA ATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGCTGTTACCGTTCCAGGAGATGG GACTGAATTAGAATTCAAACAAATTTTCCAGCGCTTCTGAGTTTTACCTCAGTCACATAATAAGGAATGCATCCCTGTGTAAGT GCATTTTGGTCTTCTGTTTTGCAGACTTATTTACCAAGCATTGGAGGAATATCGTAGGTAAAAATGCCTATTGGATCCAAAGAG AGGCCAACATTTTTTGAAATTTTTAAGACACGCTGCAACAAAGCAGGTATTGACAAATTTTATATAACTTTATAAATTACACCG AGAAAGTGTTTTCTAAAAAATGCTTGCTAAAAACCCAGTACGTCACAGTGTTGCTTAGAACCATAAACTGTTCCTTATGTGTGT ATAAATCCAGTTAACAACATAATCATCGTTTGCAGGTTAACCACATGATAAATATAGAACGTCTAGTGGATAAAGAGGAAACTG GCCCCTTGACTAGCAGTAGGAACAATTACTAACAAATCAGAAGCATTAATGTTACTTTATGGCAGAAGTTGTCCAACTTTTTGG
TTTCAGTACTCCTTATACTCT AACTAAGAATTTAAGGCTGGG CCAGAAGTTTGAGACCAGCCT GTGCCTGTAATCCCAGCTACA ATGCCACTGCACTCTAGCCTG
TAAAAATGATCTAGGACCCCCGGAGTGCTTTTGTTTATGTAGCT
CGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG GGCCAACATGGTGAAACCCTATCTCTACTAAAAATACAAAAAAT CGGGAGGTGGAGGCAGGAGAATCGCTTGAACCCTGGAGGCAGAG GGCCACATAGCATGACTCTGTCTCAAAACAAACAAACAAACAAA
Large amounts of raw DNA sequence data
TACCATATTAGAAATTTAA GTGGGCGGATCACTTGAGG GTGCTGCGTGTGGTGGTGC GTTGCAGTGAGCCAAGATC AAACTAAGAATTTAAAGTT
AATTTACTTAAAAATAATGAAAGCTAACCCATTGCATATTATCACAACATTCTTAGGAAAAATAACTTTTTGAAAACAAGTGAG TGGAATAGTTTTTACATTTTTGCAGTTCTCTTTAATGTCTGGCTAAATAGAGATAGCTGGATTCACTTATCTGTGTCTAATCTG TTATTTTGGTAGAAGTATGTGAAAAAAAATTAACCTCACGTTGAAAAAAGGAATATTTTAATAGTTTTCAGTTACTTTTTGGTA TTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCATAGGTCTTTCCCATGTCGCAACATCATGCAGTGA TTATTTGGAAGATAGTGGTGTTCTGAATTATACAAAGTTTCCAAATATTGATAAATTGCATTAAACTATTTTAAAAATCTCATT CATTAATACCACCATGGATGTCAGAAAAGTCTTTTAAGATTGGGTAGAAATGAGCCACTGGAAATTCTAATTTTCATTTGAAAG
TTCACATTTTGTCATTGACAACAAACTGTTTTCCTTGCAGCAACAAGATCACTTCATTGATTTGTGAGAAAATGTCTACCAAAT TATTTAAGTTGAAATAACTTTGTCAGCTGTTCTTTCAAGTAAAAATGACTTTTCATTGAAAAAATTGCTTGTTCAGATCACAGC TCAACATGAGTGCTTTTCTAGGCAGTATTGTACTTCAGTATGCAGAAGTGCTTTATGTATGCTTCCTATTTTGTCAGAGATTAT TAAAAGAAGTGCTAAAGCATTGAGCTTCGAAATTAATTTTTACTGCTTCATTAGGACATTCTTACATTAAACTGGCATTATTAT TACTATTATTTTTAACAAGGACACTCAGTGGTAAGGAATATAATGGCTACTAGTATTAGTTTGGTGCCACTGCCATAACTCATG CAAATGTGCCAGCAGTTTTACCCAGCATCATCTTTGCACTGTTGATACAAATGTCAACATCATGAAAAAGGGTTGAAAAAAGGA ATATTTTAATAGTTTTCAGTTACTTTTTGGTATTTTTCCTTGTACTTTGCATAGATTTTTCAAAGATCTAATAGATATACCCGA

3. Making Sense out of Sequence …

4. The Ensembl genome browser: making it interesting
The ENCODE (ENCyclopedia Of DNA Elements) project Science 306: (2004)
Genes
Variation
Regulatory elements 9

5. Vertebrate species on Ensembl
Mostly vertebrates
                   

6. Non‐vertebrates on Ensembl genomes
Fungi
Bacteria
Protists
Metazoa Plants

7. Ensembl and EnsemblGenomes

8. Ensembl gene models
Automatic annotation
Manual annotation

9. Automatic gene annotation
Genome-wide determination using the Ensembl automated pipeline
Predictions based on the genomic sequence (ab initio)
Predictions based on experimental (biological) data
ESTs
RNAseq data
cDNA and protein alignments (from sequence DBs)

10. Biological Evidence International Nucleotide Sequence databases
Protein sequence databases
Swiss-Prot: manually curated
TrEMBL: unreviewed translations
NCBI RefSeq
Manually annotated proteins and mRNAs (NP, NM)

11. Manual gene annotation
Gene determination on a case by case basis by a curator •
Genome-wide
Genes list h v

12. Ensembl automatic annotation

13. Automatic annotation
Many species (>60)
Genome-wide at once
Manual annotation
Few species (Hs, Mm, Dr)
Gene-by-gene

14. Golden transcripts Identical annotation • Higher confidence and qualitygf
3’ UTR
5’ UTR
UTR Intron Exon
Exons are drawn as boxes – filled boxes are coding and unfilled boxes are untranslated. Introns are drawn as lines.

15. CCDS transcripts Consensus coding DNA sequence set
Agreement between EBI, WTSI, UCSC and NCBI •
CCDS transcript vg

16. Higher quality transcripts
CCDS transcripts (protein-coding only)
Ensembl/Havana merged transcripts
Both a limited number of species

17. Ensembl stable IDs ENSG########### Ensembl Gene ID
ENST########### Ensembl Transcript ID
ENSP########### Ensembl Peptide ID
ENSE########### Ensembl Exon ID
For non‐human species a suffix is added:
MUS (Mus musculus) for mouse ENSMUSG###
DAR (Danio rerio) for zebrafish: ENSDARG###

18. NCBI http://www.youtube.com/ncbinlm Go to www.youtube.com
Search “NCBI tutorial general”

19. The National Center for Biotechnology Information
Bethesda,MD
Created in 1988 as a part of the National Library of Medicine at NIH
Establish public databases
Research in computational biology
Develop software tools for sequence analysis
– Disseminate biomedical information

20. Three international nucleotide sequence databases

21. Selected NCBI Databases
Biomedical literature
PubMed free Medline
PubMed Central full text online access
NCBI Bookshelf online biomedical textbooks
Biomolecular Databases
Nucleotide
GenBank submitted sequence records
RefSeq curated NCBI reference sequences
Protein GenBank and RefSeq translations, outside protein
dbSNP small scale genetic variations
Structure biomolecular 3-D structures
MMDB NCBI’s 3D structure database
GEO microarray expression data
SRA next-generation sequence data

22. GenBank & RefSeq

23. RefSeq: NCBI’s Derivative Sequence Database
Experimentally verified / curated transcripts and proteins
NM_, NP_ accession numbers
Model transcripts and proteins
XM_, XP_ accession numbers
Assembled Genomic Regions (contigs)
NT_, NW_ accession numbers
Chromosome records
NC_, AC_ accession numbers
RefSeqGene Records
NG_ accession numbers (NG_ also used pseudo genes and other fixed genomic sequences)
Draft whole genome shotgun assemblies (microbial)
NZ_ accession numbers
Microbial proteins
NP_, YP_, ZP_ accessions

24. UCSC Genome Browser

25. GeneCards