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RESEARCHatGENOME BIOINFORMATICS LAB
Josep F. Abril Ferrando and Genís Parra
Farré Genome BioInformatics Research Lab RGBI _at_
( IMIM UPF CRG )
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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 _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Computational Analysis of Genomic Sequences
DNA SEQUENCE
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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From Genes to Genomes Single Genes
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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From Genes to Genomes Chromosomes
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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From Genes to Genomes Whole Genomes
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Comparative Genomics Single Genes
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Comparative Genomics Syntenic Regions
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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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 _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Programming in POSTSCRIPT (II)
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
counter1 2nd loop mark 0.25 0.35
counter2 2nd loop mark 0.25
counter3 box mark ... repeat
finish loop (x3) pop
clean up stack (removes "mark") showpage E
OF
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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GFF2PS and GFF2APLOT
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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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.htm
l
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Whole Genome Gene-Finding
Homo sapiens
DATABASE
GENES
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Whole Genome Gene-Finding Comparative Approach
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Whole Genome Gene-Finding Comparative Approach
GENES
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Whole Genome Gene-Finding Results Analysis
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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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 _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Predicting Novel Genes in the Mouse Genome (I)
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Predicting Novel Genes in the Mouse Genome (II)
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Homology and Gene Structure Filtering
Homo sapiens Predictions
Mus musculus Predictions
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Exon Structure over an Alignment
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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RT-PCR Validation
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Results of the Experimental Validation
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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Example of a Bash Script
BIOINFORMÀTICA UPF T23 2003/03/06 J.F. Abril
and G. Parra _at_ Genome BioInformatics Lab RGBI
(IMIM-UPF-CRG)
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http//genome.imim.es/