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Ensembl Web Erin Pleasance Canada’s Michael Smith Genome Sciences Centre, Vancouver Lab 7.2 1 Homepage at http://www.ensembl.org Lab 7.2 2 Species-specific homepage Search Browse by chromosome Statistics of current release Site map Lab 7.2 3 Site Map Lab 7.2 4 Getting help Click Back to homepage Lab 7.2 5 Text search caspase-3 Lab 7.2 6 GeneView ContigView of gene ContigView of gene and surrounding region ProteinView TransView of transcript Lab 7.2 ExonView 7 GeneView (On the same page) GeneView of homologues References provided by SWISSPROT via GeneDAS ExportView Lab 7.2 GeneSNPView 8 GeneView (On the same page) Information provided for each transcript individually Links to external databases AlignView of gene against external sequence Lab 7.2 9 GeneView GOView: Gene Ontology classification of function DomainView of functional domains FamilyView of other proteins in same family TransView Lab 7.2 ProteinView 10 TransView ExonView Lab 7.2 11 ExonView Lab 7.2 12 Click Back to Lab 7.2 GeneView 13 ProteinView Links to external databases Lab 7.2 14 Click Back to Lab 7.2 GeneView 15 ContigView Chromosome and bands Sequence contigs Lab 7.2 16 ContigView Detailed View Navigation Position on chromosome Gene annotations Homologous sequences link to external databases Lab 7.2 17 ContigView Basepair View Forward strand Reverse strand • DNA sequence • 6-frame translation • Enzyme sites Lab 7.2 18 ContigView Single nucleotide polymorphisms Lab 7.2 19 SNPView Lab 7.2 20 Click Back to ContigView Markers Lab 7.2 21 MarkerView Lab 7.2 22 Click Back to ContigView Zoom out Lab 7.2 23 Forward strand ContigView of surrounding region caspase-3 Nearby genes Reverse strand “Unstranded” Lab 7.2 24 ContigView Feature tracks Explore all the menu options available! Informs that other tracks are available Lab 7.2 25 ContigView Feature tracks Repeats appear in new track Lab 7.2 26 Exporting From ContigView From GeneView Lab 7.2 27 ExportView • Flatfile (EMBL or GenBank) with features • FASTA sequence only • Feature list in a table • Image of region Lab 7.2 28 ExportView Flatfile Lab 7.2 29 Click Back to ExportView Lab 7.2 30 EnsMart Data Mining “EnsMart is a powerful data mining toolset for retrieving customised data sets from annotated genomes, using criteria from Ensembl and third party databases.” To export: • Genes • SNPs Lab 7.2 31 MartView: Start Indicates current query progress Refine query Reviews current query, indicates number of objects to be retrieved Lab 7.2 32 MartView: Filter 4 186139601 186339601 Upload gene lists Specify query requirements Lab 7.2 33 MartView: Output Can also output Output sequence, SNP info, gene structure Lab 7.2 Note number of entries 34 to be retrieved MartView: Results Lab 7.2 35 Similarity searching BLAST: for distantly related or protein sequences; slow SSAHA: for nearly identical sequences; fast Lab 7.2 36 Similarity searching: SSAHA Copy-and-paste sequence OR upload file (my_sequence.txt) Lab 7.2 37 Similarity searching: SSAHA Similar sequences on chromosomes List of results Lab 7.2 38 Similarity searching: SSAHA Results shown in ContigView Lab 7.2 39 Other access methods: AnchorView Lab 7.2 40 Other access methods: Disease View Lab 7.2 41 Other access methods: KaryoView Lab 7.2 42 Exercises Single nucleotide variations in the gene HFE have been associated with the disease hemochromatosis. • What types of annotations represent this gene (eg. Ensembl novel gene, etc.)? How many Ensembl transcripts are annotated for this gene? • How many coding SNPs are in the transcript for the longest protein product of this gene? • What is the mouse homologue of this gene? Obtain a GenBank-format file of this homologue. • How many EST transcripts appear to be equivalent to this gene? What markers overlap this gene? What is one type or repeat found in the 3’ UTR of this gene? Lab 7.2 43