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Sequence Alignments. Chi-Cheng Lin, Ph.D. Associate Professor Department of Computer Science Winona State University – Rochester Center [email protected]. Sequence Alignments. Cornerstone of bioinformatics What is a sequence? Nucleotide sequence Amino acid sequence - PowerPoint PPT Presentation
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Summer Bioinformatics Workshop 2008
Sequence Alignments
Chi-Cheng Lin, Ph.D.Associate Professor
Department of Computer ScienceWinona State University – Rochester Center
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Summer Bioinformatics Workshop 2008
Sequence Alignments Cornerstone of bioinformatics What is a sequence?
Nucleotide sequence Amino acid sequence
Pairwise and multiple sequence alignments What alignments can help
Determine function of a newly discovered gene sequence
Determine evolutionary relationships among genes, proteins, and species
Predict structure and function of protein
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Why Align Sequences? The draft human genome is available Automated gene finding is possible Gene: AGTACGTATCGTATAGCGTAA
What does it do?What does it do? One approach: Is there a similar gene in
another species? Align sequences with known genes Find the gene with the “best” match
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Visualization of Sequence Alignment Dot Plot One of the simplest and oldest methods for
sequence alignment Visualization of regions of similarity
Assign one sequence on the horizontal axis Assign the other on the vertical axis Place dots on the space of matches Diagonal lines means adjacent regions of
identity
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A Simple Example Construct a simple
dot plot for
TAGTCGATGTGGTCATC
The alignment isTAGTCGATGTGGTC-ATC
T A G T C G A T GT * * *G * * *G * * *T * * *C *A * *T * * *C *
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Genes Accumulate Mutations over Time Mistakes in gene replication
or repair Deletions, duplications Insertions, inversions Translocations Point mutations
Environmental factors Radiation Oxidation
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Codon deletion:ACG ATA GCG TAT GTA TAG CCG… Effect depends on the protein, position, etc. Almost always deleterious Sometimes lethal
Frame shift mutation: ACG ATA GCG TAT GTA TAG CCG… ACG ATA GCG ATG TAT AGC CG?… Almost always lethal
Deletions
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Indels Comparing two genes it is generally
impossible to tell if an indel is an insertion in one gene, or a deletion in another, unless ancestry is known:
ACGTCTGATACGCCGTATCGTCTATCTACGTCTGAT---CCGTATCGTCTATCT
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The Genetic Code
SubstitutionsSubstitutions are mutations accepted by natural selection.
Synonymous: CGC CGA
Non-synonymous: GAU GAA
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Point Mutation Example: Sickle-cell Disease
Wild-type hemoglobin DNA3’----CTT----5’
mRNA5’----GAA----3’
Normal hemoglobin------[Glu]------
Mutant hemoglobin DNA3’----CAT----5’
mRNA5’----GUA----3’
Mutant hemoglobin------[Val]------
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image credit: U.S. Department of Energy Human Genome Program, http://www.ornl.gov/hgmis.
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Comparing Two Sequences Point mutations, easy:ACGTCTGATACGCCGTATAGTCTATCTACGTCTGATTCGCCCTATCGTCTATCT
Indels are difficult, must align sequences:ACGTCTGATACGCCGTATAGTCTATCTCTGATTCGCATCGTCTATCT
ACGTCTGATACGCCGTATAGTCTATCT----CTGATTCGC---ATCGTCTATCT
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Scoring a Sequence Alignment Example
Match score: +1 Mismatch score: +0 Gap penalty: –1
ACGTCTGATACGCCGTATAGTCTATCT ||||| ||| || ||||||||----CTGATTCGC---ATCGTCTATCT Matches: 18 × (+1) Mismatches: 2 × 0 Gaps: 7 × (– 1)
Various scoring scheme exist.
Score = 18 + 0 + (-7) = +11Score = 18 + 0 + (-7) = +11
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How can we find an optimal alignment?
Finding the alignment is computationally hard:ACGTCTGATACGCCGTATAGTCTATCTCTGAT---TCG-CATCGTC--T-ATCT
There are ~888,000 possibilities to align the two sequences given above.
Algorithms using a technique called “dynamic programming” are used – out of the scope of this workshop.
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Global and Local Alignments Global alignments – score the entire alignment Local alignment – find the best matching
subsequence Why local sequence alignment?
Global alignment is useful only if the sequences to be aligned are very similar
Subsequence comparison between a DNA sequence and a genome
Identify Conserved regions Protein function domains
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Example Compare the two sequences:TTGACACCCTCCCAATT ACCCCAGGCTTTACACAG
Global alignment (does it look good?)TTGACACCCTCC-CAATT || || || ACCCCAGGCTTTACACAG
Local alignment (does it look good?)---------TTGACACCCTCCCAATT || |||| ACCCCAGGCTTTACACAG--------
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Where do we get sequences to work with? Biological databases
NCBI Entrez (http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=)
Wet labs Simulations Other people’s results On-line education resources
BEDROCK (http://www.bioquest.org/bedrock/) BLAST results
