How to make a phylogenetic tree with a specific bacteria in it?

08 May 2020 3 974 Report

Hello everybody,

I´m a student and have no experience with phylogenetic tree. My task is to make a phylogenetic tree of a phylum of bacteria (proteins and rna) according to photosynthesis.

There should be a specified bacteria in that tree. The problem is, that on ncbi there s only one protein of that one bacteria.

I read that you should use core proteom for taxonomic tree but thats not possible because in the ncbi databank is not enough input. So do I assume right, that there s only one phylogenetic tree with that bacteria possible?

Farhana Rumzum Bhuiyan

You can follow this.

The basic steps in any phylogenetic analysis include:

Assemble and align a dataset

The first step is to identify a protein or DNA sequence of interest and assemble a dataset consisting of other related sequences.
DNA sequences of interest can be retrieved using NCBI BLAST or similar search tools.
Once sequences are selected and retrieved, multiple sequence alignment is created.
This involves arranging a set of sequences in a matrix to identify regions of homology.
There are many websites and software programs, such as ClustalW, MSA, MAFFT, and T-Coffee, designed to perform multiple sequence on a given set of molecular data.

Build (estimate) phylogenetic trees from sequences using computational methods and stochastic models

To build phylogenetic trees, statistical methods are applied to determine the tree topology and calculate the branch lengths that best describe the phylogenetic relationships of the aligned sequences in a dataset.
The most common computational methods applied include distance-matrix methods, and discrete data methods, such as maximum parsimony and maximum likelihood.
There are several software packages, such as Paup, PAML, PHYLIP, that apply these most popular methods.

Statistically test and assess the estimated trees.

Tree estimating algorithms generate one or more optimal trees.
This set of possible trees is subjected to a series of statistical tests to evaluate whether one tree is better than another – and if the proposed phylogeny is reasonable.
Common methods for assessing trees include the Bootstrap and Jackknife Resampling methods, and analytical methods, such as parsimony, distance, and likelihood.

Akash Mahadme

Thank you very much. I have problems with identifying the protein of interest. The tree must enclude a specific bacteria (bacteria x). NCBI says that there is only 1 protein of this bacteria on ncbi. Is there any other option to get for example core proteins of this bacteria x?

Farhana Rumzum Bhuiyan

Hello Akash,

I think you can search in other databases as well to find your desired one. Ex. UniProtKB. https://www.uniprot.org/help/uniprotkb

You can go to the description of what you get and then jump to other databases to find similar sequences.

I hope it helps.

How to compare two groups with only two measurements?

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What is the best way to keep an anaerobic chamber anoxic in the absence of hydrogen?

Do we need to write protocol for a second study of a systematic review that has been registered and published?

How to increase a model accuracy ?

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

Good sites to recruit survey participants on a grad school student budget?

Sample dilution for quantitative analysis using ELISA?