Clustalw Multiple Sequence Alignment Visualization

Question

[Thaman]

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

[Giovanni M Dall'Olio]

did you mean "parsing" or "visualizing"?

[Thaman]

visualizing in specific

[Thaman]

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

Answer 1

[Tom Walsh]

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

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

[Giovanni M Dall'Olio]

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

[Thaman]

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

[Thaman]

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

[Tom Walsh]

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

[Thaman]

I tried but got application fail error

Answer 2

[Neilfws]

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.

Answer 3

[Fred Fleche]

[?]

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

Answer 4

[Giovanni M Dall'Olio]

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

• Jalview for example
• CLC Sequence Viewer by default uses lines instead of characters, so it is easier to make annotations

[Thaman]

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

[Giovanni M Dall'Olio]

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..

[Thaman]

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

[Giovanni M Dall'Olio]

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.