Whole Genome Alignment

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Whole Genome Alignment

• Adam Phillippy
• Fall 2008

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Motivation
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Breast cancer cell lines
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Goal of WGA

• For two genomes, A and B, find a mapping from
  each position in A to its corresponding position
  in B

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Global vs. Local alignments

• Global pairwise alignment
• ...AAGCTTGGCTTAGCTGCTAGGGTAGGCTTGGG...
• ...AAGCTGGGCTTAGTTGCTAG..TAGGCTTTGG...
• Whole genome alignment

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Alignment Visualization
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Global visualization
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WGA visualization

• How can we visualize whole genome alignments?
• With an alignment dot plot
• N x M matrix
• Let i position in genome A
• Let j position in genome B
• Fill cell (i,j) if Ai shows similarity to Bj
• A perfect alignment between A and B would
  completely fill the positive diagonal

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Translocation
Inversion
Insertion
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Drosophila shuffling
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Alignment Algorithms
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Alignment tools

• Whole genome alignment
• MUMmer (nucmer)
• Developed, supported and available at CBCB
• LAGAN, AVID
• VISTA identity plots
• Multiple genome alignment
• MGA, MLAGAN, DIALIGN, MAVID
• Multiple alignment
• Muscle, ClustalW
• Local sequence alignment
• BLAST, FASTA, Vmatch

open source
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MUMmer

• Maximal Unique Matcher (MUM)
• match
• exact match of a minimum length
• maximal
• cannot be extended in either direction without a
  mismatch
• unique
• occurs only once in both sequences (MUM)
• occurs only once in a single sequence (MAM)
• occurs one or more times in either sequence (MEM)

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Fee Fi Fo Fum,is it a MAM, MEM or MUM?
MUM maximal unique match
MAM maximal almost-unique match
MEM maximal exact match
R
Q
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Seed and extend with nucmer

• How can we make bigger matches?
• Find MUMs
• using a suffix tree
• Cluster MUMs
• using size, gap and distance parameters
• Extend clusters
• using modified Smith-Waterman algorithm

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Seed and extend
FIND all MUMs
CLUSTER consistent MUMs
EXTEND alignments
R
Q
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Matching

• Suffix tree
• O(n) construction
• O(n) space
• O(nm) Longest common substring
• O(1) Lowest common ancestor
• O(1) Longest common suffix-prefix
• O(nk) Find all k maximal repeats
• O(nmk) Find all k maximal matches

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Suffix Tree for atgtgtgtc
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Clustering
cluster length ?mi
gap distance C
indel factor B A / B or B A
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Extending
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score 70
Q
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Banded alignment
0
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Usage Examples
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WGA example with nucmer

• Yersina pestis CO92 vs. Yersina pestis KIM
• High nucleotide similarity, 99.86
• Two strains of the same species
• Extensive genome shuffling
• Global alignment will not work
• Highly repetitive
• Many local alignments

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COMMANDwhole genome alignment

• nucmer maxmatch CO92.fasta KIM.fasta
• -maxmatch Find maximal exact matches (MEMs)
• delta-filter m out.delta gt out.filter.m
• -m Many-to-many mapping
• show-coords -r out.delta.m gt out.coords
• -r Sort alignments by reference position
• mummerplot --large --fat out.delta.m
• --large Large plot
• --fat Nice layout for multi-fasta files
• --x11 Default, draw using x11 (--postscript,
  --png)
• requires gnuplot

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COMMANDassembly comparison

• nucmer maxmatch ASM1.fasta ASM2.fasta
• -maxmatch Find maximal exact matches (MEMs)
• ASM1 Multi-fasta file of contigs from assembly 1
• delta-filter m out.delta gt out.filter.m
• -m Many-to-many mapping
• show-coords -rcl out.delta.m gt out.coords
• -r Sort alignments by reference position
• -c Alignment coverage as a of contig length
• -l Length of aligned contig
• mummerplot --large --fat out.delta.m
• --large Large plot
• --fat Nice layout for multi-fasta files
• --x11 Default, draw using x11 (--postscript,
  --png)
• requires gnuplot

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Assembly comparison
9kb insertion
5kb translocation
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Comparative assembly

• Assembly
• Overlap, layout, consensus
• Orient and place sequencing reads
• Using overlaps and mate-pair information
• Scaffolding
• Order and orient draft contigs
• Using mate-pair information and experimental
  validation
• Comparative assembly and scaffolding
• Map, layout, consensus
• Orient and place reads and contigs
• Using a reference genome and alignment mapping
• AMOScmp

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Its easier when you know the answer
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Comparative assembly caveats
Truth
Assembly
A
B
A
B
A
B
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Human vs. Human
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Human vs. human
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Human indels
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References

• Documentation
• http//mummer.sourceforge.net
• publication listing
• http//mummer.sourceforge.net/manual
• documentation
• http//mummer.sourceforge.net/examples
• walkthroughs
• Email
• mummer-help_at_lists.sourceforge.net
• amp_at_umiacs.umd.edu

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Acknowledgements
Art Delcher
Steven Salzberg
Mihai Pop
Mike Schatz
Stefan Kurtz