Question: Clustalw Multiple Sequence Alignment Visualization
4
gravatar for Thaman
10.0 years ago by
Thaman3.2k
Finland
Thaman3.2k wrote:

As i am trying to build web application regarding sequence alignment. What are the best approaches in parsing Clustal multiple sequence alignment file so it will look more readable and clear through without long vertical scrolling in the browser.

Thanks in advance

alignment clustalw • 7.6k views
ADD COMMENTlink modified 9.4 years ago by Fred Fleche4.3k • written 10.0 years ago by Thaman3.2k

did you mean "parsing" or "visualizing"?

ADD REPLYlink written 10.0 years ago by Giovanni M Dall'Olio27k

visualizing in specific

ADD REPLYlink written 10.0 years ago by Thaman3.2k

My output looks like this and its so odd http://i48.tinypic.com/ae48ew.jpg

ADD REPLYlink written 10.0 years ago by Thaman3.2k
6
gravatar for Tom Walsh
10.0 years ago by
Tom Walsh550
United Kingdom
Tom Walsh550 wrote:

Have you considered a embedding a alignment viewer applet such as Jalview?

Full disclosure: I work in the group that develops Jalview.

ADD COMMENTlink modified 21 months ago by RamRS27k • written 10.0 years ago by Tom Walsh550

looks cool, but I don't see any button there: http://yfrog.com/2rjalviewnoappletp

ADD REPLYlink written 10.0 years ago by Giovanni M Dall'Olio27k

Sorry it should have been parsing in my own style rather then using third party application.

ADD REPLYlink written 10.0 years ago by Thaman3.2k

This looks pretty odd to me http://i48.tinypic.com/ae48ew.jpg

ADD REPLYlink written 10.0 years ago by Thaman3.2k

@giovanni: If the Jalview buttons don't appear you might need to check the Java plugin in your browser.

ADD REPLYlink written 10.0 years ago by Tom Walsh550

I tried but got application fail error

ADD REPLYlink written 10.0 years ago by Thaman3.2k
4
gravatar for Neilfws
10.0 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

If you have many sequences and restricted width, I don't see how vertical scrolling can be avoided.

One approach is to put each sequence on one line and scroll horizontally. This is how Seaview (not a web application) displays alignment and it can be quite effective, since the eye is drawn to conserved "blocks".

Another approach would be to provide the option of downloading the alignment as a text file and use a different visualisation in the browser to summarise the alignment graphically, without showing the sequences. I'm not sure how that would look, but I'm sure there are examples or ideas from other people.

ADD COMMENTlink written 10.0 years ago by Neilfws48k
3
gravatar for Fred Fleche
10.0 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

[?]

[?][?]BOXSHADE 3.21 : Pretty Printing and Shading of Multiple-Alignment files[?][?] http://ch.embnet.org/software/BOX_form.html

ADD COMMENTlink written 10.0 years ago by Fred Fleche4.3k
1
gravatar for Giovanni M Dall'Olio
10.0 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

Why don't you have a look at how other sequence/alignment visualizing programs render alignments.

ADD COMMENTlink written 10.0 years ago by Giovanni M Dall'Olio27k

What about parsing because my original approach was about parsing without long scrolling bar in the broswer

ADD REPLYlink written 10.0 years ago by Thaman3.2k

I don't understand what you say... 'parsing' means reading a file in a standard format and extracting the data from it.. I think you mean visualizing..

ADD REPLYlink written 10.0 years ago by Giovanni M Dall'Olio27k

I want to extract data and arrange them in a clear and cut way

ADD REPLYlink written 10.0 years ago by Thaman3.2k

you are asking two questions at the same time. One is how to extract data: you should open a new question and explain what is your input, how do you want to parse, with which programming language, etc.. The other question is how to visualize the results in a web application, that is what people answered here.

ADD REPLYlink written 10.0 years ago by Giovanni M Dall'Olio27k
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