Bioinformatics

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4 phases/quarters of scientific progress

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Chromosomes = cellular basis of heredity

DNA double helix = molecular basis of heredity

Mechanism by which cells read information contained in genes = biological basis of heredity

With recombinant DNA technologies of cloning and sequencing, scientists can do the same

Genomics ~ deciphering genes and entire genomes

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Total codons

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4^3 = 64

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Start codon

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ATG

AUG

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Stop codons

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TAA, TAG, TGA

UAA, UAG, UGA

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Use of fourier transform

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DNA coding sequences exhibit 3-base periodicity ~ periodicity can be modeled via fourier tranform

DNA non-coding sequences do not exhibit 3-base periodicity

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Method to measure gene expression

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microarray

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What do microarrays do

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quantifies [mRNA]

measures expression levels of thousands of genes at once

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Modernization of sanger method

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Automated

Capillary electrophoresis (no more gels)

ddNTPs with fluorophores (not radioactive)

Different bases ~ different colors

Chromatogram shows results (no more gels)

Provides information on quality and composition

Automated base calling

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speed of best sanger machines

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440 kbp/day

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speed of next gen sequencing machines

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325 Mbp/day

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steps in PCR

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denature

anneal

extension

repeat

electrophorese

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forces that change DNA over time

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genetic drift

natural selection

mutation

(recombination)

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natural selection description (4)

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More organisms are born than can survive or reproduce (struggle for existence)

Some organisms possess phenotypes (morphological, behavioral, biochemical attributes etc.) that enable them to better survive and reproduce

Variation in phenotypes that affects survival and reproduction is heritable (genetically controlled)

Individuals with favorable traits/phenotypes will survive and reproduce, thus passing these traits (and the controlling genes) along to their offspring

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phenotype altering mutations

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missense

nonsense

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fates of new mutation/allele

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lost in population

become polymorphisms

undergo fixation

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what represents evolution at the molecular level

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fates of new mutations or any alleles

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rationale for studying sequences/alignment

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Determine how pathogens harm hosts (~mechanisms of virulence)

Understand whether genes evolved due to GD or NS; may facilitate vaccine development since vaccines are best when they target antigens that change slowly

Study evolutionary history of organisms

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rationale for sequence alignment

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Available sequences often differ in length because sequencing efforts/methods are not standardized and indels

One may wish to know whether a sequenced genomic fragment is homologous to something else that has been previously sequenced and deposited into a large database (e.g. metagenomics)

Phylogenetics

Evolution of genes and genomes: rates of evolution (~ vaccine development); effects of selection on genomes; rates of transitions verses transversions; determining whether sequences are truly homologous (often ascertained by determining whether sequence similarity is greater than expected by chance): e.g. BLAST; assist in functional annotation (i.e. inferring a gene’s function based on homology to annotated genes)

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what is a sequence alignment

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arrangement of two or more DNA or protein sequences that minimizes the number of differences between them

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2 types of optimal alignment

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percent sequence identity

percent sequence similarity

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reason to give penalties

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Point mutations/substitutions

AA (residue) changes

Gaps

Gap extensions - penalty for extending a gap once its been "opened"; Most indels are greater than 1 bp, therefore extension penalties are lower than gap penalties

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what is a substitution matrix

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matrix that shows scores (+/- numerical values) applied for identities/similarities/differences between amino acids or identities/differences between nucleotides; add all individuals scores, plus gap and extension penalties to generate total alignment score (used to distinguish between optimal and suboptimal alignments)

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2 types of substitution matrices

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identity matrix

protein substitution matrix

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describe an identity matrix

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Identical NTs are given the same score (e.g., +1)

Different NTs are penalized with identical negative values (e.g., -1,000)

Internal gaps are not part of the matrix, but are penalized with a value that you think to be “fair” based on your expectations for the evolution of that gene or locus (gap penalties are not part of the matrix)

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2 types of protein substitution matrices

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PAM

BLOSSUM

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describe BLOSSUM 62

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based on consideration of common amino acid substitutions among proteins with >62% identity

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describe PAM 120

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calculated from alignments in which there have been 120 substitutions per 100 residues

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CDS

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CoDing Sequence, region of nucleotides that corresponds to the sequence of amino acids in the predicted protein. The CDS includes start and stop codons, therefore coding sequences begin with an "ATG" and end with a stop codon. In SGD, unexpressed sequences, including the 5'-UTR, the 3'-UTR, introns, or bases not expressed due to frameshifting, are not included within a CDS. Note that the CDS does not correspond to the actual mRNA sequence.

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average bacterial gene

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~1000 bp

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average eukaryotic gene

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~1200-1500 bp

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class ~ some of the smallest genomes in the planet and is an endosymbiot with bacteria

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Hodgkinia cicadicola

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Dynamic time warping

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aligning speech waveforms and subsequently scoring them

You have both voices and you extract features distinct for each voice

Essentially find distances between the two and subsequently use Dynamic Time Warping

A path is then generated that allows one to match the sequences

If they were exactly the same, you'd get an exact diagonal line

If there is variation, the line is jagged

If there is a lot of variation, the line is significantly diverge

Use varying scores for insertions/deletions

Use fixed score for gaps

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2 types of dynamic programming

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Needleman-Wunsch - global

Smith-Waterman - local