The Genome Access Course Genome Analysis

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TheGenomeAccessCourseGenome Analysis
From a 13th century French Bible
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• Genome Sequencing and Assembly
• Genome Analysis
• Genomes on Display

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Milestones in Genome Sequencing
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Hierarchical vs. Whole Genome Shotgun
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Sequencing Software Examples

• Phred base-calling
• Phrap assembler
• Cross_Match
• Consed graphical editor
• AutoFinish finishing
• FPCFinger Print Clone

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Genome Analysis

• Whole genome analysis
• Gene count
• Gene classification
• Repeat content
• Chromosomal duplications
• Multi-Genome Analysis
• Synteny
• Sequence similarity
• Gene classification comparisons

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Gene Count-How do we find genes in genomic
sequences?
Map cDNA sequences to a genome. Sim4
(http//pbil.univ-lyon1.fr/sim4.html) EST2Genome
(http//bioweb.pasteur.fr/seqanal/interfaces/est2g
enome.html) Genomewise BLAT
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Finding Genes Cont.
Gene Predictions Fgenesh (http//www.softberry.
com) GenemarkHMM (http//opal.biology.gatech.edu/
GeneMark/eukhmm.cgi) Genscan (http//genes.mit.ed
u/GENSCAN.html) Grail (http//compbio.ornl.gov/Gr
ail-1.3/) Glimmer (http//www.tigr.org/softlab/gl
immer/glimmer.html) Homology blastx
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Gene Prediction Types
Known cDNA evidence/homology Putative Gene
prediction which has homology to
known gene Unknown EST matching a gene
prediction Hypothetical Gene prediction(s)
only
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Gene Classification

• Automated
• Similarity search against an annotated database
• Swiss-Prot
• Nr
• Protein Domain search
• i. Pfam (http//www.sanger.ac.uk/Software/Pfam/)
• ii. Prosite
• iii. Prints
• iv. Prodom
• v. Interpro (http//www.ebi.ac.uk/interpro/scan.ht
  ml)

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Gene Classification Cont.

• 2) Curated
• Similar to above but usually people will verify
  results through literature searches

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Looking for Repeats

• RepeatMasker can find and mask repeats in DNA
  sequence
• RepeatMasker can be found at http//woody.embl-hei
  delberg.de/repeatmask/ or http//repeatmasker.geno
  me.washington.edu/
• 3. RepeatMasker is often run on genomic sequences
  before doing gene predictions

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Comparative Genome Analysis

• MUMmer
• PipMaker
• Vista

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MUMmer

• Whole genome alignments
• Compares closely related sequences
• Maximally Unique Matching subsequences
• agctcgatGGGCTTTAGACTCTCGATAggcgcagagGCTCGCTAGAATCG
  CTAGATCac
• agacctaaGGGCTTTAGACTCTCGATAagtctatccGCTCGCTAGAATCG
  CTAGATCta

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Segmentally duplicated regions in the Arabidopsis
genome, detected using MUMmer
Individual chromosomes are depicted as horizontal
grey bars (with chromosome 1 at the top),
centromeres are marked black. Coloured bands
connect corresponding duplicated segments.
Analysis of the genome sequence of the flowering
plant Arabidopsis thaliana. 2000.Nature
408796-815
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PIPMaker

• PIP stands for Percent Identity Plot
• Graphical view of similarity between two or more
  sequences
• http//bio.cse.psu.edu/pipmaker/

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Alignment
PIP Plot
Dot Plot
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Fugu PTEN
2-6
A
B
1
7
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9
5
100
100
H. sapiens
50
50
M. musculus
D. melanogaster
C. briggsae
C. elegans
A. thaliana 2
A. thaliana 3
L. major
S. pombe
2kb
4kb
6kb
8479
1
X. laevis
1239
1
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Vista

• Similar to PipMaker
• http//www-gsd.lbl.gov/vista/

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Genomes on Display

• UCSC Browser
• Ensembl browser
• NCBI Browser
• GMOD

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UCSC Browser

• http//genome.ucsc.edu

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Ensembl Browser

• http//www.ensembl.org/

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NCBI Browser

• http//www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_src
  h?chrhum_chr.infquery

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GMOD

• Generic Model Organism Database
• Attempt to make a common set of tools for
  databases/browsers for various species
• www.gmod.org

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