Course information

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Course information

• To reach meBarry Cohen
• bcohen_at_cs.njit.edu
• GITC 3802W 400-530 F 300-430www.cs.njit.edu
  /bcohen
• Web site, chat, web board, schedulemy.njit.edu
  (no www)

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Projects

• Team projects (4 person)
• One hour presentations
• Literature review / algorithms / programs
• Sample applications
• Open problems
• Homework

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Texts

• Intro to BioinformaticsLesk
• Current Topics in Computational Molecular
  BiologyJiang, Xu, Zhang

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Watson Crick, 1953
http//www.nature.com/genomics/human/watson-crick/
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Stylized double helix
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Replication

• It has not escaped our notice that the specific
  pairing we have postulated immediately suggests a
  possible copying mechanism for the genetic
  material.

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Sequence to structure
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The information cycle
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The triplet code
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In the beginning

• Life began when the earth was young
• Life arose from simple chemistry(most life still
  is relatively simple)
• Universal common ancestor
• Common molecular machinery(oldest fossils are
  living fossils)

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What is life?

• Information and metabolism
• RNA world hypothesis
• DNA as program file(information coding for
  activity)
• Replication (information which codes for itself)
• Variation, evolution(life adapts to its
  environment)

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DNA

• DNA is a polymer (sequence, string)
• DNA is composed of just four kinds ofchemical
  units (A, C, G, T)
• DNA is redundant (double helix)As pair with
  Us, Gs pair with Ts
• Some DNA codes for RNA, proteins(exons
  expressed regions)
• Some DNA is noncoding (introns intervening
  regions)
• Coherent sets of DNA are genes

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RNA

• RNA is a also polymer (sequence, string)
• RNA is composed of just four kinds ofchemical
  units (A, C, G, U)
• RNA is single stranded
• Some RNA codes for proteins,some is functional
  (e.g., tRNA)

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Proteins

• Proteins account for most life activity
  andstructure
• A protein is a polymer (sequence, string)
• Proteins are composed of 20 kinds ofchemical
  units (amino acids)
• Proteins fold into a specific shape, which
  determines their function
• Proteins are made from genetic templates(they
  dont code)

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Evolution

• Darwin evolution is adaption
• Nature has no aim, it is a result of random
  events
• Most events are DNA string edits(indels,
  substititions)
• Some events are on higher level
  structures(e.g., chromosomes)

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The tree of life

• Some errors is replication divide gene poolsinto
  two (speciation). (Or vice versa.)
• These bifurcations give the history of life a
  tree-like structure

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rRNA universal tree of life
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Algorithms

• An algorithm is a precise set of instructions for
  solving a problem (what do we mean by precise?)
• An algorithm must terminate
• Algorithms operate on data (inputs)
• Algorithms use data structures

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Data structures

• A string is a natural mathematical model of a
  biological sequence
• A directed acyclic graph may represent familial
  descent
• A tree may represent species relations

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Efficiency

• Bigger problems take more time and/or space
  (biology problems are often big)
• Harder problems take longer or more space (many
  biology problems are hard)
• Time (space), as a function of size, measures the
  complexity of an algorithm
• Many computable are problems intractable

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Complexity classes

• Search a sorted list log n
• Sort by comparison n log n
• Text search n
• Polynomial v. exponential time
• NP-complete problems

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Probability

• Base molecular events in evolution occur with a
  certain probability (frequency)
• Probability models predict what may occur
  (likelihood of a pair of jacks)
• Probability models may also infer what most
  likely has occurred

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Entropy

• Entropy is a measure of information content
• How many y/n questions are needed to get an
  answer?
• DNA positions differ in entropy, depending on how
  conserved they are