Hands-on Session 2: Obtaining Data from On-line Sources Katherine - - PowerPoint PPT Presentation

▶
hands on session 2 obtaining data from on line sources
SMART_READER_LITE
LIVE PREVIEW

Hands-on Session 2: Obtaining Data from On-line Sources Katherine - - PowerPoint PPT Presentation

Nov 28, 2023 43 likes •340 views

Hands-on Session 2: Obtaining Data from On-line Sources Katherine St. John Lehman College and the Graduate Center City University of New York stjohn@lehman.cuny.edu Katherine St. John City University of New York 1 Session Organization

slide-1
SLIDE 1

Hands-on Session 2: Obtaining Data from On-line Sources

Katherine St. John Lehman College and the Graduate Center City University of New York stjohn@lehman.cuny.edu

Katherine St. John City University of New York 1

slide-2
SLIDE 2

Session Organization

  • Goal: To be comfortable building trees from real data
  • Lecture:

– Standard Software Packages – Details on Web-based Software – Motivating Problem

  • Lab:

– Organized so you can use the DIMACS lab, or your own laptop – Welcome to work singly or in groups

Katherine St. John City University of New York 2

slide-3
SLIDE 3

Lecture Outline

  • Motivating Problem
slide-4
SLIDE 4

Lecture Outline

  • Motivating Problem
  • Building Trees Overview
slide-5
SLIDE 5

Lecture Outline

  • Motivating Problem
  • Building Trees Overview
  • Using Sequence Databases
slide-6
SLIDE 6

Lecture Outline

  • Motivating Problem
  • Building Trees Overview
  • Using Sequence Databases
  • Aligning Sequences

Katherine St. John City University of New York 3

slide-7
SLIDE 7

Motivating Problem: Building Trees with Serial Data?

Rodrigo et al., “Coalescent estimates of HIV-1 generation time in vivo.” PNAS ‘99

Katherine St. John City University of New York 4

slide-8
SLIDE 8

Motivating Problem: Using Serial Data

  • Rodrigo et al. includes 55 HIV-env partial sequences,

all from the same patient

  • Starting question: what is the genealogy samples (from

the same patient) taken at different times?

Katherine St. John City University of New York 5

slide-9
SLIDE 9

Building Trees

  • 1. Get data (from wet lab, authors, genBank, etc).
slide-10
SLIDE 10

Building Trees

  • 1. Get data (from wet lab, authors, genBank, etc).
  • 2. Align and/or filter data.
slide-11
SLIDE 11

Building Trees

  • 1. Get data (from wet lab, authors, genBank, etc).
  • 2. Align and/or filter data.
  • 3. If needed, choose the appropriate model of evolution.
slide-12
SLIDE 12

Building Trees

  • 1. Get data (from wet lab, authors, genBank, etc).
  • 2. Align and/or filter data.
  • 3. If needed, choose the appropriate model of evolution.
  • 4. Use software program(s) to build trees.
slide-13
SLIDE 13

Building Trees

  • 1. Get data (from wet lab, authors, genBank, etc).
  • 2. Align and/or filter data.
  • 3. If needed, choose the appropriate model of evolution.
  • 4. Use software program(s) to build trees.
  • 5. Analyze Results.
slide-14
SLIDE 14

Building Trees

  • 1. Get data (from wet lab, authors, genBank, etc).
  • 2. Align and/or filter data.
  • 3. If needed, choose the appropriate model of evolution.
  • 4. Use software program(s) to build trees.
  • 5. Analyze Results.

We’ll focus on the first two today.

Katherine St. John City University of New York 6

slide-15
SLIDE 15

Using PubMed

An on-line index of scientific papers: Can search by all standard methods...

Katherine St. John City University of New York 7

slide-16
SLIDE 16

Sequence Databases

  • GenBank: repository of sequences from NCBI (NIH).
  • As of August 2005, GenBank had 100 gigabases of

sequences.

  • Almost all sequences from published articles are there,

and can be located by their unique accession number

  • r PubMed ID.

Katherine St. John City University of New York 8

slide-17
SLIDE 17

LANL HIV Databases

  • Los Alamos National Laboratory maintains databases
  • f sequences, resistance, immunology, and vaccine

trials.

  • Can be searched in numerous ways including accession

number or PubMed ID.

Katherine St. John City University of New York 9

slide-18
SLIDE 18

Aligning Sequences

  • Before building a tree, the similar regions of the

sequences need to be aligned.

slide-19
SLIDE 19

Aligning Sequences

  • Before building a tree, the similar regions of the

sequences need to be aligned.

  • One of the most common alignment programs is

ClustalW: – Available via multiple servers including EBI & the Pasteur Institute – Does a global multiple sequence alignment

Katherine St. John City University of New York 10

slide-20
SLIDE 20

Getting Started

  • Find the Rodrigo et al. paper on PubMed.
slide-21
SLIDE 21

Getting Started

  • Find the Rodrigo et al. paper on PubMed. Download

the paper, and note it’s PubMed ID (PMID).

  • Use the PMID to find the sequences in the HIV

Sequence Database.

slide-22
SLIDE 22

Getting Started

  • Find the Rodrigo et al. paper on PubMed. Download

the paper, and note it’s PubMed ID (PMID).

  • Use the PMID to find the sequences in the HIV

Sequence Database.

  • Use ClustalW to align the sequences.
slide-23
SLIDE 23

Getting Started

  • Find the Rodrigo et al. paper on PubMed. Download

the paper, and note it’s PubMed ID (PMID).

  • Use the PMID to find the sequences in the HIV

Sequence Database.

  • Use ClustalW to align the sequences.
  • Using your favorite phylogenetic reconstruction

method, build a tree from the sequences.

slide-24
SLIDE 24

Getting Started

  • Find the Rodrigo et al. paper on PubMed. Download

the paper, and note it’s PubMed ID (PMID).

  • Use the PMID to find the sequences in the HIV

Sequence Database.

  • Use ClustalW to align the sequences.
  • Using your favorite phylogenetic reconstruction

method, build a tree from the sequences.

  • Analyze resulting trees

Katherine St. John City University of New York 11

slide-25
SLIDE 25

Hints:

  • Choose the ”fast” tree building option for ClustalW.
slide-26
SLIDE 26

Hints:

  • Choose the ”fast” tree building option for ClustalW.
  • To use a distance based method, you need to create a

distance matrix (dnadist) to give to the method (ie BioNJ or QuickTree).

slide-27
SLIDE 27

Hints:

  • Choose the ”fast” tree building option for ClustalW.
  • To use a distance based method, you need to create a

distance matrix (dnadist) to give to the method (ie BioNJ or QuickTree).

  • At the Pasteur Institute site, at each step, you can

choose the next step, without reloading the file.

slide-28
SLIDE 28

Hints:

  • Choose the ”fast” tree building option for ClustalW.
  • To use a distance based method, you need to create a

distance matrix (dnadist) to give to the method (ie BioNJ or QuickTree).

  • At the Pasteur Institute site, at each step, you can

choose the next step, without reloading the file. For example, after returning the distance matrix, you have the option of applying a method to the matrix.

Katherine St. John City University of New York 12

slide-29
SLIDE 29

Helpful Websites

  • Dataset for this tutorial:

http://comet.lehman.cuny.edu/stjohn/dimacsTutorial

  • PubMed & Genbank:

http://www.ncbi.nlm.nih.gov/entrez

  • HIV Sequence Database:

http://hiv-web.lanl.gov/content/index

  • The Pasteur Institute:

http://bioweb.pasteur.fr/intro-uk.html

Katherine St. John City University of New York 13