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R ESEARCH at G ENOME B IOINFORMATICS L AB

R ESEARCH at G ENOME B IOINFORMATICS L AB. Josep F. Abril Ferrando and Genís Parra Farré Genome BioInformatics Research Lab RGBI @ ( IMIM – UPF – CRG ). SUMMARY. Introduction Visualization of Genomic Annotations Comparative Genomics Human and Mouse Genomes Exon Structural Selection.

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R ESEARCH at G ENOME B IOINFORMATICS L AB

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  1. RESEARCHatGENOMEBIOINFORMATICSLAB Josep F. Abril Ferrando and Genís Parra Farré Genome BioInformatics Research Lab RGBI @ ( IMIM – UPF – CRG )

  2. SUMMARY Introduction Visualization of Genomic Annotations Comparative Genomics Human and Mouse Genomes Exon Structural Selection BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  3. Sequencing Assembling ASSEMBLED SEQUENCE Analyzing ANNOTATED SEQUENCE Computational Analysis of Genomic Sequences DNA SEQUENCE BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  4. From Genes to Genomes: Single Genes BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  5. From Genes to Genomes: Chromosomes BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  6. From Genes to Genomes: Whole Genomes BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  7. Comparative Genomics: Single Genes BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  8. Comparative Genomics: Syntenic Regions BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  9. Programming in POSTSCRIPT (I) % %% Function Definition: sub box(x,y) {...} /box { %%% y x box gsave % 20 mul % y X 0 % y X 0 moveto % y 20 mul % Y dup % Y Y 10 0 % Y Y 10 0 rlineto % Y Y 0 % Y Y 0 exch % Y 0 Y rlineto % Y -10 0 % Y -10 0 rlineto % Y neg % -Y 0 % -Y 0 exch % 0 -Y rlineto % closepath % 0 1 0 % 0 1 0 setrgbcolor % "green-color" fill % grestore % } def % Vector Graphics Language • Prefix Notation • Stacks: exec, paths, dicts, ... • Dictionaries: Identifier Object %!PS % %% Variable Definition: $counter = 0 /counter 0 def BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  10. Programming in POSTSCRIPT (II) % %% Initialization 100 100 translate % New Coords Origin 2 5 scale % Re-scaling x-axes*2 % % y-axes*5 % %% BaseLine gsave % 0 0 moveto % 90 0 lineto % 0 setgray % 1 setlinewidth % stroke % grestore % % %% Main Loop mark % mark 0.25 0.35 0.15 % mark 0.25 0.35 0.15 counttomark % mark 0.25 0.35 0.15 3 { %%%%%%%%%%%%%% begin loop (x3) /counter %% counter %% 1 add %% def %% $counter = $counter + 1 counter % % 1st loop: mark 0.25 0.35 0.15 counter==1 % 2nd loop: mark 0.25 0.35 counter==2 % 2nd loop: mark 0.25 counter==3 box % mark ... } repeat %%%%%%%%%%%%%% finish loop (x3) pop % clean up stack (removes "mark") % showpage %%EOF%% BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  11. GFF2PS and GFF2APLOT BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  12. Visualizing Genomic Annotations J.F. Abril and R. Guigó. " gff2ps: visualizing genomic annotations " Bioinformatics 16(8):743-744 (2000). M.G. Reese, G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril and S.E. Lewis. " Genome Annotation Assessment in Drosophila melanogaster " Genome Research 10(4):483-501 (2000). M.D. Adams et al (including J.F. Abril). " The Genome Sequence of Drosophila melanogaster " Science 287(5461):2185-2195 (2000). J.C. Venter et al (including J.F. Abril and R. Guigó). " The Sequence of the Human Genome " Science 291(5507):1304-1351 (2001). R.A. Holt et al (including J.F. Abril and R. Guigó). "The Genome Sequence of the Malaria Mosquito Anopheles gambiae " Science 298(5591):129-149 (2002). http://genome.imim.es/software/gfftools/GFF2PS.html BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  13. ab initio homology Whole Genome Gene-Finding Homo sapiens DATABASE GENES BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  14. Whole Genome Gene-Finding: Comparative Approach BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  15. Homo sapiens Mus musculus homology homology gene prediction gene prediction GENES Whole Genome Gene-Finding: Comparative Approach GENES BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  16. Whole Genome Gene-Finding Results Analysis BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  17. Human and Mouse Comparative Genomics Mouse Genome Sequencing Consortium (including J.F. Abril, G. Parra and R. Guigó). "Initial sequencing and comparative analysis of the mouse genome" Nature 420(6915):520-562 (2002). G. Parra, P. Agarwal, J.F. Abril, T. Wiehe, J.W. Fickett and R. Guigó. "Comparative gene prediction in human and mouse" Genome Research 13(1):108-117 (2003). R. Guigó, E.T. Dermitzakis, P. Agarwal, C.P. Ponting, G. Parra, A. Reymond,J.F. Abril, E. Keibler, R. Lyle, C. Ucla, S.E. Antonarakis and M.R. Brent. "Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes" PNAS 100(3):1140-1145 (2003). BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  18. golden path annotations golden path annotations additional blastn matches to ENSEMBL + REFSEQ additional blastn matches to ENSEMBL + REFSEQ Predicting “Novel” Genes in the Mouse Genome (I) BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  19. additional blastn matches to ENSEMBL + REFSEQ tblastx tblastx geneid exons sgp genes Predicting “Novel” Genes in the Mouse Genome (II) BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  20. Homology Blastp StructuralAlignment Exstral GENESEnriched Pool Homology and Gene Structure Filtering Homo sapiens Predictions Mus musculus Predictions BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  21. Exon Structure over an Alignment BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  22. RT-PCR Validation BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  23. Results of the Experimental Validation BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  24. Example of a Bash Script BIOINFORMÀTICA UPF T23 – 2003/03/06 – J.F. Abril and G. Parra @ Genome BioInformatics Lab – RGBI (IMIM-UPF-CRG)

  25. http://genome.imim.es/

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