Question: Interpreting distance from clustal omega
0
gravatar for Natasha
2.6 years ago by
Natasha40
Natasha40 wrote:

The phylogenetic tree obtained from multiple sequence alignment using Clustal Omega is in the following link, From what I read, I understand the values at each node represent the distance. But, I am not able to interpret these distances to quantitatively find out which sequence is close to ALDOA of humans. Any help would be highly appreciated.

alignment • 5.8k views
ADD COMMENTlink modified 2.6 years ago by Antonio R. Franco4.5k • written 2.6 years ago by Natasha40
1
gravatar for Antonio R. Franco
2.6 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

You can read information about Clustal Omefa from the authors of this program to which I sent a message claiming some information. From this message you can get the idea that Clustal Omega does not provide you with a truly phylogenetical alignment. If you need an phylogenetical alignment, I recommend to use another program like ClustalW, Muscle, Cofee, etc. To get the phylogenetical distances, you need to run bootstrapping, and you can do it using IQ-tree, for example

Clustal Omega is only a multiple sequence alignment program. It is not a phylogenetic program. Consequently there is no bootstrapping in Clustal Omega. We do use trees in Clustal Omega, but they are guide-trees, I repeat, not phylogenetic trees. Guide-trees are used to define the order in which pair-wise alignments are performed. The pair-wise alignments are done in Clustal Omega using HMMs. The clustering in Clustal Omega (in default mode) is achieved by I am not aware of any program that uses exactly the same clustering approach as Clustal Omega. My suggestion is to use Clustal Omega to produce a multiple sequence alignment and then use any suitable program to estimate a phylogentic tree. ClustalW has the capability to estimate a phylogenetic tree and calculate bootstrap values. Hope that helps. Best wishes, Fabian.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Antonio R. Franco4.5k

I believe however, that it is much better to use Clustal Omega that a truly phylogenetical program if protein functions are compared, because Clustal Omega cluster sequences together based on sequence similarity and not by phytlogenetical relationships

You can not run bootstrapping easily with Clustal Omega, but the program can be set to a maximum of 5 iteraction in its settings

ADD REPLYlink written 2.6 years ago by Antonio R. Franco4.5k

Thank you very much for the detailed explanation.I am not really able to follow what this means "To get the phylogenetical distances, you need to run bootstrapping, and you can do it using IQ-tree" and how this can be done.My knowledge of sequence alignment and bootstrapping is really limited.Kindly excuse me for the naive question. As suggested, I used ClustalW to generate the following information,

(
(
(
sp|P04075|ALDOA_HUMAN:0.01019,
sp|P00883|ALDOA_RABIT:0.00629)
:0.00704,
(
(
(
sp|P05062|ALDOB_HUMAN:0.01854,
sp|P79226|ALDOB_RABIT:0.01168)
:0.00876,
(
sp|P00884|ALDOB_RAT:0.01809,
sp|Q91Y97|ALDOB_MOUSE:0.00664)
:0.00841)
:0.18311,
(
(
sp|P09972|ALDOC_HUMAN:0.00641,
tr|G1T652|G1T652_RABIT:0.00458)
:0.00422,
(
sp|P09117|ALDOC_RAT:0.01122,
sp|P05063|ALDOC_MOUSE:0.00807)
:0.01508)
:0.07275)
:0.07685)
:0.00532,
sp|P05065|ALDOA_RAT:0.00618,
sp|P05064|ALDOA_MOUSE:0.00206);

I am not able to understand how distance information can be inferred from the above result. Any help would be much appreciated.

ADD REPLYlink written 2.6 years ago by Natasha40

Every time you build up a tree, the tree will be different. So there is when bootstrapping helps

By boostrapping, you run the same aligment lets say 1000 times. If you see that two proteins are clustered 100% of the time in the 1000 tree alignments, then you get the confidence that their relationship is a strong one. But if you see that only 10% of the alignments reproduce between two proteins, then you can think on the contrary

Bootstrapping needs a program that run the 1000 alignments and keep the percentage of cases where proteins cluster together. Clustal Omega does not include bootstrapping and I am not aware of a program able to run the same clustering algorithm that Clustal Omega uses. That's one point. So the only chance you have is to set the maximum iteraction in the configuration of Clustal Omega which I believe is 5

By the other hand you need to see clearly whether you want to cluster sequences together by phylogenetical or by sequence similarity. If phylogenetical rules apply, then Clustal Omega should not be your choice. Use ClustalW, Coffee, Muscle or even IQ-Tree that will make the boostrapping easy for you

Hoping that everything has been clarified this time

ADD REPLYlink written 2.6 years ago by Antonio R. Franco4.5k

Thank you very much for the clarification. I want to cluster the sequences by similarity. For instance, while performing pairwise alignment using Clustal Omega, percentage similarity and percentage identity are obtained. I would like to ask whether this can be obtained with multiple sequence alignment. Once again, thank you very much for your time and attention.

ADD REPLYlink written 2.6 years ago by Natasha40
0
gravatar for Antonio R. Franco
2.6 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

One more thing. After using CLustal Omega, go to the Results Summary tab and download the *ph file

Thus, you can use FigTree to better represent this tree. After playing a little bit with this program, you will see distances represented in a better way

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Antonio R. Franco4.5k

Thank you very much. The phylogenetic tree obtained is here Could you please explain what do the values represent? For instance, from the figure I wish to understand the distance from ALDOA of rabbit to ALDO A of human; ALDOA of mouse to ALDO A of human. I'm not sure on how to calculate this from the values displayed in the figure.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Natasha40

It is not an easy task to estimate the distance between proteins that are separated within a tree See this document to get an idea

This is not a question that the values you have calculated can be summed or substracted

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Antonio R. Franco4.5k

I was assuming these values can somehow be summed or subtracted. Thanks a ton for the clarification

ADD REPLYlink written 2.6 years ago by Natasha40
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