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

ClassicalPhylogenetics

MolecularPhylogeneticsHomology

Big pictureBig pictureEvolution

Divergent Convergent

Orthologs Paralogs

AnalogyHomology

Systematics

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

HomologyHomology

Speciation

Duplication

CBA

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

ParsimonyParsimonyWorking principle that prefers the least complex

explanation for an observation

Figure from http://www.cartoonchurch.com/cartoons/large/simple-living-cartoon.gif

Classical phylogeneticsClassical phylogeneticsMethod of parsimony analysis used to

develop cladograms explaining evolutionary relationships.

Fig 1. Hypothetical cladogram

Constructing cladogramsConstructing cladograms

CB

A

F

E

D

G

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

Possible cladogramsPossible cladograms

….which one do you pick?

Homoplasy & subjective Homoplasy & subjective characterscharacters

A faulty assignment of primary homology

Figure from: http://www.blackwellpublishing.com/ridley/images/analogies.jpg

Things to considerThings to consider

• Auxillary Principle

• Congruence Test

More things to considerMore things to consider

• Weighting–Needs to respond to homoplasy

• Independent characters

http://ksuoncampus.com/2008/01/29/evolution-of-mario/

Molecular PhylogeneticsMolecular Phylogenetics

• Goal:– to infer process from

pattern

• Why– Not just the observables

– Alternative method to derive evolutionary relationships

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

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

List of alignment softwareList of alignment software

Sequence AlignmentSequence Alignment

• Types–Pairwise alignment

–Multiple sequence alignment

Figure from http://en.wikipedia.org/wiki/Sequence_alignment

Human Molecular Genetics, 2006, Vol. 15, Review Issue 1, R54

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

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.

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

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?

BLASTBLAST

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

HomologeneHomologene

Aligning GenesAligning Genes

Homologene scoringHomologene scoring

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

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

Needleman-Wunsch algorithmNeedleman-Wunsch algorithm

Figure from Journal of Medical Physics 39 (2006) pg 29

Needle-wunsch algorithmNeedle-wunsch algorithm

BLAST alignBLAST align

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

ClustalW @ EBIClustalW @ EBI

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

SRD5A2 @ TreeFAMSRD5A2 @ TreeFAM

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

ProsPros ConsCons

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

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