Homology assessment and molecular sequence alignment.
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Transcript of Homology assessment and molecular sequence alignment.
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Homology assessment and Homology assessment and molecular sequence alignment.molecular sequence alignment.
Chris Stewart and Ka Yi LingChris Stewart and Ka Yi Ling
Genetics 677 Genetics 677
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ClassicalPhylogenetics
MolecularPhylogeneticsHomology
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Big pictureBig pictureEvolution
Divergent Convergent
Orthologs Paralogs
AnalogyHomology
Systematics
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HomologyHomology1. Equal in position and details
in structure
2. Equal in developmental origin (i.e. cellular/tissue structure)
3. Logical and continual series of character state transformations
Figure from http://images-eu.amazon.com/images/P/0895262002.01.LZZZZZZZ.jpg
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HomologyHomology
Speciation
Duplication
CBA
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CharacterCharacterTrait from group of organisms, which has
two or more independent states that can be evaluated
http://www.choose-life.org/Map_states_color.jpg
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ParsimonyParsimonyWorking principle that prefers the least complex
explanation for an observation
Figure from http://www.cartoonchurch.com/cartoons/large/simple-living-cartoon.gif
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Classical phylogeneticsClassical phylogeneticsMethod of parsimony analysis used to
develop cladograms explaining evolutionary relationships.
Fig 1. Hypothetical cladogram
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Constructing cladogramsConstructing cladograms
CB
A
F
E
D
G
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MatrixMatrixSegmented Jawed Hair Placenta Multi-cell Limbs
Cat
Kangaroo
Lizard
Salmon
Earthworm
Sponge
Amoeba
1 1 1 1 1 1
1 1 1 0 1 1
0 0 0 0 1 0
1 0 0 0 1 0
1 1 0 0 1 0
1 1 0 0 1 1
0 0 0 0 0 0
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Possible cladogramsPossible cladograms
….which one do you pick?
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Homoplasy & subjective Homoplasy & subjective characterscharacters
A faulty assignment of primary homology
Figure from: http://www.blackwellpublishing.com/ridley/images/analogies.jpg
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Things to considerThings to consider
• Auxillary Principle
• Congruence Test
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More things to considerMore things to consider
• Weighting–Needs to respond to homoplasy
• Independent characters
http://ksuoncampus.com/2008/01/29/evolution-of-mario/
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Molecular PhylogeneticsMolecular Phylogenetics
• Goal:– to infer process from
pattern
• Why– Not just the observables
– Alternative method to derive evolutionary relationships
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Sequence alignment programs
Figure modified from http://bioinfo.ochoa.fib.es/docus/courses/Ali2005Filogenias/seq_analysis/images/SeqAnalFloChart.gif
Protein or Gene of interest
Sequence alignment programs
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Molecular charactersMolecular characters
• What can be used? – Nucleotide sequences– Protein sequences– DNA– RNA– Protein
• NO single universally accepted recipe
Figure from http://www.ittc.ku.edu/bioinfo_seminar/images/wheel.gif
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List of alignment softwareList of alignment software
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Sequence AlignmentSequence Alignment
• Types–Pairwise alignment
–Multiple sequence alignment
Figure from http://en.wikipedia.org/wiki/Sequence_alignment
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Human Molecular Genetics, 2006, Vol. 15, Review Issue 1, R54
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The nuts and bolts The nuts and bolts
1.1. Gene/ protein of Gene/ protein of interestinterest
2. Homolog search
3. Sequence alignment
4. Tree building
Figure from http://www.usingneuralnetworks.com/images/Face_But_Not_The_Name_Cartoon.jpg
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Database Search: BLASTDatabase Search: BLAST
• Basic Local Alignment Search Tool
• Input: Protein and Nucleotide
• Default algorithm: Blosum62
• Other algorithms: PAM family, Blosum family
• Sites that use BLAST: NCBI, EBI, GenomeNet, PIR, DDBJ
Figure: NCBI alignment result site.
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How does BLAST score an alignment?How does BLAST score an alignment?
Default matrix in BLAST 2.0
BLOSUM= BLOcks Substitution Matrix
Based on local alignments
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BLOSUM62: contributions from proteins more than 62% identical are weighted to sum to one.
Scores: Number values
How does BLAST score an alignment?How does BLAST score an alignment?
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BLASTBLAST
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The nuts and bolts The nuts and bolts
1. Gene/protein of interest
2.2. Homolog searchHomolog search
3. Sequence alignment
4. Tree building
Figure from http://www.usingneuralnetworks.com/images/Face_But_Not_The_Name_Cartoon.jpg
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HomologeneHomologene
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Aligning GenesAligning Genes
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Homologene scoringHomologene scoring
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The nuts and bolts The nuts and bolts
1. Gene/protein of interest
2. Homolog search
3.3. Sequence Sequence alignmentalignment
4. Tree building
Figure from http://www.usingneuralnetworks.com/images/Face_But_Not_The_Name_Cartoon.jpg
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Pair-alignment
• Algorithm: Needleman-wunsch dynamic programming
• Global alignment
• DNA, protein
• Find positional
primary homology
• Sites that use N-W: EBI server
Figure from http://ww2.cs.fsu.edu/~hui/research/scanalyze_tutorial/pics/registered_group.jpg
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Needleman-Wunsch algorithmNeedleman-Wunsch algorithm
Figure from Journal of Medical Physics 39 (2006) pg 29
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Needle-wunsch algorithmNeedle-wunsch algorithm
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BLAST alignBLAST align
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Multiple sequence alignmentMultiple sequence alignment
• Example: ClustalW
• Progressive alignment
• Nucleotide and Protein
sequences
• Local or Global alignment
• Sites that use MSA: EBI, DDBJ, PBIL, EMBNet, GenomeNet
Figure from www.cs.umbc.edu
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ClustalW @ EBIClustalW @ EBI
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The nuts and bolts The nuts and bolts
1. Gene/protein of interest
2. Homolog search
3. Sequence alignment
4.4. Tree buildingTree building
Figure from http://www.usingneuralnetworks.com/images/Face_But_Not_The_Name_Cartoon.jpg
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SRD5A2 @ TreeFAMSRD5A2 @ TreeFAM
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DiscussionDiscussion
• Does sequence orthology relate to functional equivalence?
• Can paralogs be functionally related?
• Do unsequenced genomic regions affect the understanding of orthology and paralogy?
Figures from: http://www.ndpgenderequality.ie/images/cartoons/cartoon_large_intro.gif and http://www.faithmouse.com/cartoon567.jpg
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ProsPros ConsCons
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Pros and consPros and cons
• Best guess
• Parsimony
• Algorithms
• Speed vs accuracy
• Evolution vs religion
• Evolutionary history
• Find animal models
• Relation between structure and function
• Biological processes
Figure from: http://www.pbrainprojects.com/images/angel_devil.jpg
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Assumptions, assumptions, Assumptions, assumptions, assumptionsassumptions
• If Xs is true then the tree is true…
Figure from: http://www.gdargaud.net/Humor/Pics/string_theory.png
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