CSHL course on Computational Genomics, November 5-11, 2003 Lisa Stubbs and Ivan Ovcharenko, "Algorithms for Genome Comparison"; Sunday, November 9th

Comparative Sequence Analysis Tools
	http://www.dcode.org ECR Browser @ http://ecrbrowser.dcode.org - alignments of the human, mouse, rat, fugu, tetraodon, and zebra-fish genomes rVista @ http://rvista.dcode.org - identification of evolutionary conserved transcription factor binding sites zPicture @ http://zpicture.dcode.org - dynamic alingment and visualization of conservation profiles

1. Aligning sequences to identify evolutionary conserved regions

Identify regulatory elements of the DLX cluster

- select multi-zPicture tool on the main zPicture web page - choose 3 sequences to align - Upload human chr2:173148317-173176043 and rat chr3:53729585-53754455 regions from the UCSC browser - add fugu homologous sequence that you can download from here - select Dynamic visualization option at the results web page - 2 elements that are conserve in all the species are known regulatory elements of this cluster (Ghanem N. et al., Genome Research, 2003 Apr;13(4):533-43)

2. Browsing genomes using synteny links

Visualize conservation profile of the GATA3 gene in human, mouse and rat genomes

- search for GATA3 gene using the ECR Browser - select "Synteny/Alignment" link to identify homologous regions from other species - click on the location link from one of the species to have this specie as a base genome - identify rodent specific ECRs (Evolutionary Conserved Regions)

3. Designing primers/oligos

Design 50nts oligo for the first upstream ECR of the IL4 gene

- search for IL4 gene using the ECR Browser - zoom out - click on Grab ECR button, then on the conserved element - click on "design oligos for the human sequence" - set 26 to 28 GC count in 50nts - select one of the oligos and test uniqueness of it in the human and mouse genomes

4. Aligning sequences to vertebrate genomes

Align one of the draft rabbit BACs to the human genome, obtain conservation plot

- select GENOME ALIGNMENT feature of the ECR Browser - request a download of a draft rabbit BAC from the NCBI that has AC145542.1 accession number - proceed and align it to the human genome - use Dynamic visualization to obtain a conservation profile and Dot-plot feature to order and orient contigs

5. Assigning function to regulatory elements

One of the NPP (natriuretic peptide precursor) genes located on the human chromosome 1 is being synergistically regulated by TBX5 and NKX2.5 transcription factors. Identify this gene and the regulatory element

- locate all the NPP genes in the human genome by using the ECR Browser and searching for "NPP" - select one of the genes on the human chromosome 1 - zoom into the NPP cluster on the human chromosome 1 (mouse click on the browser image recenters the browser) - run rVista on this region using "Synteny/Alignment" link - select TBX5 and NKX25 transcription factor binding sites to look for - click on the "Visualization" link at the rVista results web page

Questions or comments?

Please don't hesitate to forward them to either Lisa Stubbs (stubbs5@llnl.gov) or Ivan Ovcharenko (dcode@ncbi.nlm.nih.gov)