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Browsing Genes and Genomes with Ensembl Genome Browser

Mamoona Mushtaq: mamoona.mushtaq@hgen.slu.se Saima Zubair: saima.zubair@hgen.slu.se Department of Animal Breeding and genetics. Browsing Genes and Genomes with Ensembl Genome Browser. Introduction Interactive tutorial Assignment. Outline. Ensembl Genome browser http://www.ensembl.org

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Browsing Genes and Genomes with Ensembl Genome Browser

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  1. Mamoona Mushtaq: mamoona.mushtaq@hgen.slu.se Saima Zubair: saima.zubair@hgen.slu.se Department of Animal Breeding and genetics Browsing Genes and Genomes with Ensembl Genome Browser

  2. Introduction • Interactive tutorial • Assignment Outline

  3. Ensembl Genome browser http://www.ensembl.org • Joint project b/w EBI & Welcome Trust Sanger Institute • Started in 2000 with the completion of HGP • Funded primarily by the Wellcome Trust, additional funding by EMBL, NIH-NIAID, EU, BBSRC and MRC INTRODUCTION

  4. Provide annotation for the biological community that is freely available and of high quality • Display the integrated picture of whole genome assemblies, their comparisons & functionally important coding and non-coding sequences Ensembl’sAIM

  5. The gene set: Automatic annotation based on mRNA and protein information • Programmatic access via the Perl API (open source) • BioMart • Integration with other databases • Comparative analysis (gene trees) Features

  6. Focuses on chordates • Includes genome of > 50 species • Most popular species: Human, mouse, rat & Zebra fish • More than half of chordates are mammals • The non-chordate genomes like C.elegans, yeast & fruit fly are also included and aid in more accurate phylogenetic trees Ensembl Species

  7. Ensembl analysis now expanded to bacteria, plants, protists and fungi • Sister Project: www.ensemblgenomes.org Ensembl Sister Project

  8. Not created by Ensembl, instead provided by other institutes/consortia, e.g • NCBI  human, mouse • Rat Genome Sequencing Consortium  rat • Sanger  zebrafish • Broad Institute  mammals • Baylor College  cow • Washington University  chicken Genome Assemblies

  9. Genome assembly + • Experimental evidence + mRNA/Protein • Computer programs Ensembl Genes

  10. Uniprot/Swiss-Prot A manually curated database, of highest accuracy • NCBI RefSeq A partially manually curated database • UniProt/TrEMBL Automatically annotated translations of EMBL coding sequence (CDS) features • EMBL/GenBank/DDBJ Primary nucleotide sequence repository Ensembl Gene Evidence

  11. Ensembl known transcripts • Ensembl novel transcripts • Ensembl merged transcripts (HAVANA) • EST clusters • More manual curation (SGD, WormBase, FlyBase) Genes and Transcripts in Ensembl

  12. ENSG### Ensembl GeneID • ENST### Ensembl TranscriptID • ENSP### Ensembl Peptide ID • ENSE### Ensembl ExonID • For other species than human a suffix is added: MUS (Musmusculus) for mouse: ENSMUSG### DAR (Daniorerio) for zebrafish: ENSDARG### IDs in Ensembl

  13. Gene Annotation: Available Annotations

  14. Transcript Annotation:

  15. Peptide Annotation:

  16. IDs in other Databases: See IDs from other databases against Ensembl Gene ID through “External References”

  17. Cytogenetic band A banding pattern on a chromosome resulting from staining and examination by microscopy Marker A short sequence whose placement on the genome is known Repeat Repetitive DNA in which the same sequence occurs multiple times

  18. Comparative Data: • Orthologues • Paralogues • Protein families • Whole genome alignments • Syntenicregions

  19. Variation Data: (SNPs)

  20. Regulatory data: Set of regulatory elements for particular gene Data from external sources (DAS)

  21. View genes along with other annotation along the chromosome • View alternative transcripts for a gene • Explore homologues and phylogenetic trees across more than 50 species for any gene • Compare whole genome alignments and conserved regions across species • View microarray sequences that match to Ensembl genes • View ESTs, clones, mRNA and proteins for any chromosomal region • Examine SNPs for a gene or chromosomal region Synopsis-What can I do with Ensembl

  22. View SNPs across strains (rat, mouse), populations (human) or even breeds (dog) • View positions and sequence of mRNA and protein that align with an ensembl gene • Upload your own data • Use BLAST, or BLAT, a similar sequence alignment search tool, against any Ensembl genome • Export sequence, or create a table of gene information with BioMart • Use the Variant Effect Predictor

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