Generating Multiple Sequence Alignments with ClustalW

Slides:

Advertisements

Similar presentations

Classification of Organisms

Advertisements

Phylogenetic Tree A Phylogeny (Phylogenetic tree) or Evolutionary tree represents the evolutionary relationships among a set of organisms or groups of.

Evolutionary Analysis. Tree Mathematical structure Model evolutionary history.

Reading Phylogenetic Trees Gloria Rendon NCSA November, 2008.

Section 17.2 Summary – pages

NCBI National Center for Biotechnology Information.

BIO2093 – Phylogenetics Darren Soanes Phylogeny I.

Reading Phylogenetic Trees

Phylogeny and Systematics

First release of HOGENOM, a database of homologous genes from complete genome Equipe Bioinformatique et Génomique Evolutive Laboratoire de Biométrie et.

Phylogeny and Systematics By: Ashley Yamachika. Biologists use systematics They use systematics as an analytical approach to understanding the diversity.

Multiple sequence alignment and alignment editor.

CHAPTER 25 TRACING PHYLOGENY. I. PHYLOGENY AND SYSTEMATICS A.TAXONOMY EMPLOYS A HIERARCHICAL SYSTEM OF CLASSIFICATION  SYSTEMATICS, THE STUDY OF BIOLOGICAL.

Multiple Sequence Alignments and Phylogeny.  Within a protein sequence, some regions will be more conserved than others. As more conserved,

Are Euglena plants or animals?. NEITHER! Euglena are protists: a single celled, eukaryotic organism Some euglena have chloroplasts Some euglena are highly.

Systematics the study of the diversity of organisms and their evolutionary relationships Taxonomy – the science of naming, describing, and classifying.

The Evolutionary History of Biodiversity

 Fossils provide an objective record of Evolution Fossil = A preserved or mineralized remains (bone- petrified tree – tooth – shell) or imprint of an.

Applied Bioinformatics Week 8 Jens Allmer. Practice I.

Chapter 8 Molecular Phylogenetics: Measuring Evolution.

PHYLOGENETIC TREES. A phylogeny, or species/evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms,

Reading Phylogenetic Trees

Wednesday, September 11, 2013 TAKE OUT: Bioinformatics pre-lab (p. 1-2); tear off pages 3-8 from lab handout AND RECYCLE ! SAVE analysis questions on page.

Orthology & Paralogy Alignment & Assembly Alastair Kerr Ph.D. [many slides borrowed from various sources]

Using blast to study gene evolution – an example.

Phylogenetic analysis taken from and es/MSAPhylogeny.htm.

Orthology & Paralogy Alignment & Assembly Alastair Kerr Ph.D. WTCCB Bioinformatics Core [many slides borrowed from various sources]

Applied Bioinformatics Week 8 Jens Allmer. Theory I.

Gene models and proteomes for Saccharomyces cerevisiae (Sc), Schizosaccharomyces pombe (Sp), Arabidopsis thaliana (At), Oryza sativa (Os), Drosophila melanogaster.

While hiking, a student decided to collect and eat berries from the plants he came across on the AT trail. Unfortunately, he became very ill and had to.

Chapter 26 Phylogeny and the Tree of Life

Introduction to Bioinformatics Resources for DNA Barcoding

Phylogenetic basis of systematics

Classification of Organisms

Unrooted phylogenetic tree showing the relationship between the human SLC2A gene family for all 14 members created using PHYLIP 3.6 softwareDistance between.

Pipelines for Computational Analysis (Bioinformatics)

Sequence and structure relatedness of matrix protein of human respiratory syncytial virus with matrix proteins of other negative-sense RNA viruses K.

5.4 Cladistics.

Multiple Alignment and Phylogenetic Trees

Office hours aplenty...

Classification and The Tree of Life

Evolution of Biodiversity

Cladistics Cladistics: classification based on common ancestry

Evidence and Phylogenetic trees

Phylogenetic Trees and Cladograms

Phylogeny and Systematics

Explore Evolution: Instrument for Analysis

Reading Phylogenetic Trees

Generating Multiple Sequence Alignments with Clustal Omega

Phylogeny and Systematics LECTURE #33

Chapter 19 Molecular Phylogenetics

Phylogeny and Systematics (Part 6)

Multiple sequence alignment & Phylogenetics Analysis

Phylogenetic analysis of replication proteins expressed by bifidobacterial plasmids. Phylogenetic analysis of replication proteins expressed by bifidobacterial.

Identification of novel F-box proteins in Xenopus laevis

Sequence and structure relatedness of matrix protein of human respiratory syncytial virus with matrix proteins of other negative-sense RNA viruses K.

Volume 10, Issue 14, Pages R512-R513 (July 2000)

Molecular data assisted morphological analyses

Phylogenetic Trees and Cladograms

Phylogenetic Trees Jasmin sutkovic.

PHYLOGENETIC TREES.

Chapter 26 Phylogeny and the Tree of Life

Chapter 20 Phylogeny and the Tree of Life

Comparing DNA Using Blast

Phylogeny and the Tree of Life

Phylogenetic Trees Vocab

Phylogenetic analysis reveals a protozoan-specific clading of TgATPaseP-GC. Phylogenetic analysis reveals a protozoan-specific clading of TgATPaseP-GC.

Neighbor-joining tree of the 262 S

1 2 Biology Warm Up Day 6 Turn phones in the baskets

Multiple alignment of type I and III IFNs from Xenopus, chicken, and human. Multiple alignment of type I and III IFNs from Xenopus, chicken, and human.

Presentation transcript:

Generating Multiple Sequence Alignments with ClustalW

ClustalW: creating a multiple sequence alignment You identify sequences to align Get Fasta sequences and copy and paste into window or put all sequences in one document and attach (example: copy and paste into one Word document)

ClustalW: Creating the initial alignment

ClustalW: The Alignment Report

ClustalW: The Alignment Report

ClustalW: The Alignment Report

ClustalW: The Alignment Report

ClustalW: Jalview

ClustalW: Jalview

ClustalW: Jalview

ClustalW: creating a phylogenetic tree ClustalW can only assemble a phylogenetic tree from multiple sequence alignments generated by ClustalW

ClustalW: Making a Phylogenetic Tree

ClustalW: Making a Phylogenetic Tree

ClustalW: Making a Phylogenetic Tree

ClustalW: Making a Phylogenetic Tree Must use Clustal aligned sequences & include “Clustal” line

ClustalW: Making a Phylogenetic Tree

ClustalW: Making a Phylogenetic Tree Phylogram: tree that provides an estimate of a phylogeny, where the branch lengths are proportional to the amount of evolutionary divergence. Cladogram: tree that provides an estimate of phylogeny where the branches are of equal length: therefore cladograms indicate common ancestry, but do not reflect amount of evolutionary time separating sequences.  

ClustalW: The Phylogram Tree

ClustalW: The Cladogram Tree

ClustalW: Practice Weblem Align the refseq protein sequences of Arabidopsis thaliana RDR6, Schizosaccharomyces pombe Rdp1, Caenorhabditis elegans rrf-2, Caenorhabditis elegans rrf-3, and Aspergillus fumigatus Sad-1 using ClustalW. Print out this alignment. Generate and print out a phylogram and cladogram using this alignment. Given what you know about the evolutionary relationships between these organisms, does the phylogram and cladogram make sense? Why or why not?