Construction of Phylogenetic tree based on Gamma Fibrinogen

Posted Tue, 02/24/2009 - 05:20

Phylogenetic Tree of different species based on Gamma Fibrinogen

A phylogenetic tree or evolutionary tree is a tree showing the evolutionary relationships among various biological species or other entities that are believed to have a common ancestor. There are many different types of trees:

* dendrogram - broad term for the diagrammatic representation of a phylogenetic tree.
* cladogram - formed using cladistic methods, only represents a branching pattern, i.e., branch lengths do not represent time.
* phylogram - explicitly represents number of character changes through its branch lengths.
* ultrametric tree or chronogram - explicitly represents evolutionary time through its branch lengths.[1]

Gamma Fibrinogen is a protein which functions in platelet activation, signal transduction and protein polymerisation.[2]

The following strategy is based on the presence of this protein in different species and their relationship with each other based on the presence of this protein.

* Go to www.uniprot.org (protein sequence and functional information database)

* Click Retrieve to get a sequences of a list of entries

* Enter the following Accession numbers in the retrieve window:

O12957 (Sheep)
O02672 (Moose)
O02683 (Giraffe)
O02690 (Chevrotain)
O02681 (Beluga)
O02687 (Sperm_Whale)
O02673 (Rorqud)
O02688 (Pig)
O12959 (Pecari)
O02677 (Dromedary)
O02689 (Tapir)
O02682 (Horse)
O02676 (Hyena)
O02680 (Coyote)
O12954 (Hippopotamus)

* Click Open under the Download Data; FASTA option

* FASTA sequence of all the entries is retrieved.

* Copy and paste this in Notepad and save it as Gamma_Fibrinogen

* Write the name of each species as given above in the FASTA format obtained after the accession number of each species.

* Go to www.ebi.ac.uk/clustalw (general purpose multiple sequence alignment program for DNA or proteins)

* Select “fast” in Alignment (You may choose to run a full alignment or using a stringent algorithm for generating the tree guide or a fast algorithm)

* Select “input” in Output Order (Decide which order the sequences should be printed in the alignment)

* Upload the FASTA file (Gamma_Fibrinogen.txt)

* Click Run

* In the results of CLUSTAL W, click View Alignment File.

* Copy and paste the results in the same Gamma_Fibrinogen.txt file under the FASTA sequence

* Go back to www.ebi.ac.uk/clustalw

* Select “fast” in Alignment

* Select “input” in Output Order.

* Select “NJ” in Tree Type.

* Select “on” in Correct Distance.

* Select “on” in Ignore Gaps (With this option, any alignment positions where ANY of the sequences have a gap will be ignored. This means that 'like' will be compared to 'like' in all distances. It also, automatically throws away the most ambiguous parts of the alignment, which are concentrated around gaps (usually). The disadvantage is that you may throw away much of the data if there are many gaps) [4]

* Paste the Alignment sequence obtained after CLUSTAL

* Run

* In the CLUSTAL results, click Show as Phylogram Tree

* Click Show Distances

* Go to http://bioweb2.pasteur.fr/phylogeny/intro-en.html

* Under the option of Computation of Distance click Protdist

* Enter your email address in the bar provided on the top left side of the page

* In the Bootstrap options select Random Number Seed to be 3 and Replicates to be 2. Bootstrap is a method used to check the reliability of a tree. Greater the bootstrap value higher will be the reliability of the tree.

* Paste the FASTA sequences of the species retrieved earlier

* Click Run.

* In the results page, select “neighbor” in the scroll down menu under protdist.outfile.

* Click Further Analysis

* Check Neighbor-Joining method.

* Set Outgroup Species as 4

* Click Run.

* In the results a Neighbor output Tree file is obtained which gives the newick format that can be used together with TreeView to obtain a phylogenetic tree.