CS 461b661b: Bioinformatics Tools and Applications

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CS 461b/661b Bioinformatics Tools and
Applications
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• Bin Ma
• Title Associate Professor
• Research area Bioinformatics
• Office hours Tuesday 4-5pm, Wednesday 4-5pm.
• Office MC362

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Bioinformatics
Bioinformatics
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Class Time

• Monday, MC320, 230-430pm
• Wednesday, MC320/MC325, 330-430pm
• Jan. 7. An overview session.
• Jan. 14 (Monday), 16 (Wednesday) will be lectured
  by Mark Daley.

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Evaluation

• Two assignments (10 marks each)
• One project (30 marks)
• One final exam (50 marks)

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• TA ??.

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Topic Whole Genome Shotgun Sequencing

• Sequencing machines are used to read small
  fragments. Then the reads are assembled
  together.
• How to cut and clone.
• How sequencing machines work.
• How to assemble.
• DIY assemble a small genome.

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Topic PCR and Primer Design

• How to select a region of DNA and make millions
  of copies rapidly.
• How to design the primers.
• Use it to identify the criminals by FBI and
  polices.
• DIY design a primer

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Topic Gene prediction
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Gene prediction

• How translation is done
• Gene structures
• How to find genes, the most interesting parts on
  a genome.
• DIY find a gene using software.

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Topic NCBI Entrez

• Where to get biological data.
• Use Entrez as a comprehensive data source.
• DIY download and compare sequences of the same
  protein in 20 different mammals.

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Topic BLAST and PatternHunter
GCNTACACGTCACCATCTGTGCCACCACNCATGTCTCTAGTGATCCCTCA
TAAGTTCCAACAAAGTTTGC

GCCTACACACCGCCAGTTGTG-TTCCTGCTATGTCTCTAGTGAT
CCCTGAAAAGTTCCAGCGTATTTTGC GAGTACTCAACACCAACATTGA
TGGGCAATGGAAAATAGCCTTCGCCATCACACCATTAAGGGTGA----

GAATACTCAACAGCAACATCAAC
GGGCAGCAGAAAATAGGCTTTGCCATCACTGCCATTAAGGATGTGGG -
-----------------TGTTGAGGAAAGCAGACATTGACCTCACCGAGA
GGGCAGGCGAGCTCAGGTA

TTGACAGTACACTCATAGTGTTGAGGAAAGCTGACGTTGACCTCACC
AAGTGGGCAGGAGAACTCACTGA GGATGAGGTGGAGCATATGATCACC
ATCATACAGAACTCAC-------CAAGATTCCAGACTGGTTCTTG

GGATGAGATGGAACGTGTGATGACCAT
TATGCAGAATCCATGCCAGTACAAGATCCCAGACTGGTTCTTG
sequence alignment
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Homology Search

• Use NCBI BLAST as a tool to find similarities.
• Spaced seeds.
• How to implement the spaced seeds as computer
  programs.
• DIY Experiment the sensitivity comparison
  between spaced seeds and BLAST seed.

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Mass Spectrometry

• Genomics ? Proteomics
• Proteins are more directly related to the
  functions of cells
• Many diseases are closely related to abnormal
  proteins
• Knowing which proteins are present in different
  cells under different conditions is useful
• Protein ID becomes an essential task in proteomics

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Tandem mass spectrometry

• Tandem mass spectrometry (MS/MS, tandem MS) is
  the standard way for protein identification.

tandem mass spectrometer
peptide
MS/MS spectrum
LSIMQDK
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Mass Spectrometry

• Principles of instruments
• Noises and complications in the data
• De novo sequencing
• SPIDER (de novo sequencing homology search)
• DIY
• Use a mass spec to identify a protein
• Use PEAKS software to determine a peptide
• Use SPIDER software to identify a protein

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High Performance Liquid Chromatography (HPLC)
liquid (water etc.)
after 20 minutes or so
to ESI MS/MS
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• DIY predict the retention time of a few peptides.

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Protein Quantitation

• Several different methods for quantitation using
  mass spec.
• DIY use a spectrum to determine the relative
  quantity of two proteins.

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Next Generation Sequencing

• How to sequence an individual humans whole
  genome (3G bps) in one day, using less than 1000
  dollars.
• Huge impact on personalized medicine.