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Explore Evolution: Instrument for Analysis

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Presentation on theme: "Explore Evolution: Instrument for Analysis"— Presentation transcript:

1 Explore Evolution: Instrument for Analysis
Adapted from ppt by Graziela Valente Krizia Cabrera Toro

2 History MEGA The first version was distributed to over 2000 scientists. MEGA2 It was a complete rewrite of the first version to take advantage of the manifold increase in computing power of the average desktop computer and the availability of the Microsoft Windows graphical interfaces. MEGA3 Sequence data alignment and assembly features. Web browser. MEGA4 different registered s

3 bacteriology and general disease, plant biology, conservation biology,
MEGA is used in diverse disciplines, including: AIDS/HIV research, virology, bacteriology and general disease, plant biology, conservation biology, systematics, developmental evolution, and population genetics.

4 MEGA is an integrated tool for :
mining web-based databases automatic and manual sequence alignment, inferring phylogenetic trees, estimating rates of molecular evolution, and testing evolutionary hypotheses.

5 Download MEGA from: http://www.megasoftware.net/mega4
MEGA is an easy to use computer program with an extensive user-friendly interface.

6 Sequence Acquisition and Alignments
Sequence alignment is usually the first step in comparative sequence analysis. Building these alignments involves a few steps including: Acquisition of sequences from databanks Computational sequence alignments Manual fine-tuning of the initial alignment

7 Data acquisition Most scientists obtain gene sequences from databanks using a web browser. MEGA now includes an integrated web-browsing facility. Homologous sequences are usually searched by: gene name or Genbank accession number Blast procedure ( to find sequences with sequence similarity) In both cases a set of sequences are found and displayed on the screen Once the list of desired sequences are generated click on “ADD TO ALIGNMENT” in the MEGA web browser. MEGA then parses the sequences automatically and sends them to Alignment Explorer.

8 Computational sequence alignments

9 Create a new Alignment

10 DNA or Protein?

11 Retrieving Sequences from WEB

12 Query Genbank

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16 Send to Text

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19 Sequence Data added to Alignment Explorer from NCBI
Each row represents a single sequence Each column represents a site Identity across all sequences is indicated by a “*”

20 Copy/Paste sequences To/From Clipboard

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24 Edit the Sequence name

25 Delete sequences

26 Insert New Sequences – MEGA/FASTA/TEXT files

27 BLAST sequences from alignment directly

28 Adding new sequences to an existing alignment

29 Alignment

30 Select Data to be aligned
MEGA allows the alignment of different regions independently

31 MEGA has the ability to align any user-selected region

32 ClustalW Parameters: ability to select all options
ClusterW is the most widely used multiple sequence alignment system for DNA and protein Data

33 Data aligned Identity across all sequences is indicated by a “*”

34 Save as MEGA file for direct analysis in MEGA

35 MEGA Format

36 FASTA Format

37 Save alignment session for future display

38 Retrieve sequences from a file

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40 Motif Searching

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42 Highlighting

43 Highlighting and Aligning

44 Sequence Alignment Construction
Retrieving sequences From the web to “Create a new alignment” adding new sequences to an existing alignment Blast sequences from alignment From the Files “Open a saved alignment session” Retrieving a file with sequences to be aligned Multiple sequences aligning using ClustalW manual alignment any user-selected region Save and Export data Recognizing different formats: Mega format “ .meg” Fasta format “.fas” DNA or Protein Translate data DNA - Amino acid Motif searching/highlighting

45 Open Saved Data

46 Conserved sites

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48 Construct Phylogeny

49 Questions can address to the instructor at exploreevolution@outlook
Questions can address to the instructor at


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