Research Article |
Open Access |
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Methodology for Phylogenetic Tree Construction |
Kudipudi Srinivas 2, Allam Appa Rao 1, GR Sridhar 3, Srinubabu Gedela 1 * |
1International Center for Bioinformatics & Center for Biotechnology, Andhra University, 530 003, India |
2Dept of Computer Science, Acharya Nagarjuna University, Nagajuna Nagar-522 010 |
3Endocrine and Diabetes Centre, Krishna Nagar, Visakhapatanam, 530 002, India |
| *Corresponding author: |
Dr. Srinubabu Gedela,
Email: srinubabuau6@gmail.com |
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| Received April 20, 2008; Accepted May 15, 2008; Published May 25, 2008 |
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Citation: Kudipudi S, Allam AR, Sridhar GR, Srinubabu G (2008) Methodology for Phylogenetic Tree Construction. J Proteomics Bioinform S1: S005- S011. doi:10.4172/jpb.s1000002 |
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Copyright: © 2008 Kudipudi S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution
License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and
source are credited. |
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| It has been our endower to present and explore different steps involved in the construction of a phylogenetic tree using online
services. The application of different bioinformatic tools is necessary for the realization of the desirable results. A stepwise
construction strategy using on line ClustalW is proposed with suitable application. The method can hope fully will aid the reader
to construct the phylogenetic tree. Construction of phylogenetic tree is useful for comparison of homology of functional proteins
in one species and between species. |
Keywords
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| Protein; DNA; FASTA; BLAST |
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| Introduction |
| Tree representation of the family history of set of sequences that
share a common ancestor is called a Phylogenetic Tree. A phylogeny
tree shows the connection among various organisms and
weight of the branches in the tree indicates time between evolutions
of different organisms. |
Uses of Phylogenetic Tree
• Determining the relatives of the organisms and interested.
• Identify the functionality of a gene
• Trace the origin of a gene |
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Material and Methods |
1. Retrieving Required Sequence (Protein/DNA) from Major
Databases. |
1.1. Retrieving Protein sequence using major Protein databases. |
Major Protein databases are |
Protein Information Resource(PIR) http://pir.georgetown.edu/
Swiss-Prot http://us.expasy.org/sprot
Example to retrieve required Protein sequence from Swiss-Port
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| 1.1.1 |
Open the link at to http://www.expasy.org/sprot/
sprot-search.html |
| 1.1.2 |
Type required protein/gene sequence name in the
Gene name window , and click the Submit Query
button. |
| 1.1.3 |
Select the required gene from given result and
click |
| 1.1.4 |
To get the FASTA format, Click the FASTA format
button , on the extreme right of the entry. |
| 1.1.5 |
Save the Sequence into your PC |
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1.2. Retrieving DNA sequence using major Nucleotide
Sequence databases |
Major Nucleotide Sequence databases are |
• European Molecular Biology Laboratory
(EMBL) http://www.ebi.ac.uk/
• GenBank (National Center for Biotechnology
Information, NCBI) http://www.ncbi.nlm.nih.gov/
• DNA databank of Japan (DDBJ) http://
www.ddbj.nig.ac.jp/ |
2. Using BLAST to Compare Sequence of Interest (Protein/
DNA) to other Sequences |
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| 2.1 |
Open the link at to www.ncbi.nlm.nih.gov/BLAST |
| 2.2 |
Click the Standard Nucleotide-nucleotide
BLAST[blastn]/Standard Protein-Protein
BLAST[blastp] Ex: Click Standard Protein-Protein BLAST[blastp] |
| 2.3 |
Open the Saved FASTA-formatted sequence(Protein/
DNA) from the PC |
| 2.4 |
Copy and Paste into the BLAST Searching window |
| 2.5 |
Deselect the Do CD-Search box. |
| 2.6 |
If you use Protein Sequence don’t change the Choose
Database setting, because the nr (for non redundant) is
the default protein database |
| 2.7 |
Click the BLAST! Button |
| 2.8 |
Click the Format button |
| 2.9 |
When the results page appear, scroll down the page
until you reach along list of sequences and save all
these sequences into your PC |
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3. Preparing your Multiple Sequence Alignment |
To compute your multiple sequence alignment, any of the
following can be used |
• ClustalW : www.ebi.ac.uk/clustalW/Index.html
• Dialign : www.bibiserv.techfak.uni-bielefeld.de/
dialing
• Tcoffee : www.igs-server.cnrs-mrs.fr/Tcoffee
Steps to produce multiple sequence using EBI ClustalW server |
| 3.1 |
Open the link at the EBI ClustalW server at
www.ebi.ac.uk/clustalW/Index.html |
| 3.2 |
Paste the collected sequences from the sequence window |
| 3.3 |
Use Output format pull-down menu to set the selection of choice |
| 3.4 |
Choose Input from the Output Order pull-down
menu. When output order set to input, ClustalW
outputs your sequence in their original order. If the
output order is set to aligned, the sequence appears in
the order of they are aligned. |
| 3.5 |
Click the Run Button at the bottom of page. |
| 3.6 |
Save your results. Results come in three sections. First
one is Pairwise section, second one is the multiple
Alignment and third one is guide tree. |
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4. Computing the Tree |
Use the following methods to construct the Phylogenetic Tree |
• ClustalW
• Phylip |
Steps involved in a phylogenetic tree using online EBI
ClustalW server |
| 4.1 |
Open the link at the EBI ClustalW server at
www.ebi.ac.uk/clustalW/Index.html |
| 4.2 |
Paste your Multiple alignment into sequence window. |
| 4.3 |
Choose NJ from Phylogenetic Tree: Tree Type drop
down menu |
| 4.4 |
Choose On from Correct Dist. Drop-down menu. |
| 4.5 |
Choose On from the Ignore Gaps drop-down menu |
| 4.6 |
Choose Phylogram from the Tree drop-down menu |
| 4.7 |
Click the Run Button and view the tree. |
| 4.8 |
Results are saved |
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Phylogenetic Tree Construction of Butyrylcholinesterase |
1. Retrieving Bche Gene Sequence from Swiss-Port |
a. Point your browser to http://www.expasy.org/
sprot/sprot-search.html |
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| b |
Type Gene name Bche in Gene name window ,Homo sapiens in Organism window and click the Submit Query button. |
| c |
http://www.expasy.org/cgi-bin/get -
entries ? d b = s p & d b = t r & D E = & G Nc=AND&GN=Bche &OC=Homo+sapie
ns&wild=1&view=full&num=100 |
| d |
Select the required gene from given result. For Ex: P06276 and get the FASTA format and save. |
| e |
http://www.expasy.org/uniprot/P06276 |
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2. Using BLAST to Compare P06276 Gene Sequence to other Sequences |
a. Point your browser to www.ncbi.nlm.nih.gov/
BLAST . Click the Standard Protein-Protein
BLAST[blastp] |
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b. Paste P06276 FASTA formatted sequence in the
sequence window
c. Press Format Option if your request has successfully
executed |
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d. Select required sequence and Save into your PC |
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3. Prepare Multiple Sequence Alignment with ClustalW for P06276 |
a. Point your browser to the EBI ClustalW server
www.ebi.ac.uk/clustalW/Index.html |
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b. Paste colleted sequences in the sequence window
c Click the Run Button at the bottom of page. |
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d. Save your results |
2. Computing your Tree Using ClustalW Method for
P06276. |
a. Point your browser to the EBI ClustalW server
www.ebi.ac.uk/clustalW/Index.html
b. Paste Multiple Sequence alignment into sequence
window .
c. Choose NJ from Phylogenetic Tree: Tree Type drop
down menu |
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d. Choose On from Correct Dist. Drop-down menu,
Choose On from the Ignore Gaps drop-
down
menu,Choose Phylogram from the Tree drop-down
menu and Click the Run Button and view the tree. |
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Conclusion |
For phylogenetic tree construction, the essential performance
parameters have been discussed here in detail to provide guidance
to computational biologists. In particular, the stepwise discussion
strategy is a very attractive goal, and this methodology,
which, if appropriately used, can solve several problems and constitutes
a powerful tool in the hands of researchers. The aim of
this article, with application to Phylogenetic tree construction of butyrylcholinesterase has been contribute to a further research
studies for homology comparison of functional proteins in species. |
Acknowledgment |
This work was supported by IIT up gradation grants of AUCE
(A). |
