Monday, January 19, 2009

Dot Plot

The article like the article below titled "Sequence Alignment Techniques" is related to the field of Bioinformatics. In the field of Bioinformatics Sequence Matching and Sequence Alignment play an important roll. By using Dot Plot we can do Sequence Matching, people of other fields can also view this article as a novel method of matching a pair of words.



Let us view the procedure-
Suppose we have 2 sequences,
Sequence1- ACCTGGAAA
Sequence2- AGGTCCAPP

Place Sequence1 on X axis and Sequence2 on Y axis
Figure1- The Matrix






Compare each element of X axis and Y axis, plot a point whenever same element occurs.



Figure2- Plotting of points





Now join, the points with diagonal lines.

Figure3- Joining of points which occur in diagonal boxes



I am a student of Bioinformatics, below I have written a code in PERL language which can generate a Dot Plot between any 2 sequences, this PERL code will be a useful reference for graduate and undergraduate student of Bioinfomatics.

THE CODE
(Uploaded on 22/4/2009)


* Note- My dear friend, if you are downloading the code kindly include a comment. Your comments mean a lot to me and will encourage me to write more.

11 comments:

Mohit Soni said...

Thanks a lot. It was useful. You can also sometime drop by on my blog: http://codebasket.blogspot.com/

Anonymous said...

Your blog keeps getting better and better! Your older articles are not as good as newer ones you have a lot more creativity and originality now keep it up!

Anonymous said...

hi mr cheetan
im a student doing bioinformatics and was wondering if you could make your code easier to download.I read what you wrote and i think your code is going to help me loads.please? k thank you.

Anonymous said...

Genial dispatch and this post helped me alot in my college assignement. Say thank you you for your information.

Anonymous said...

Hello. And Bye.

eco lodge said...

Hi buddy, firstly I would like to send greetings to all readers then I think that this information is amazing and very entertainment information, I was looking information about Dot Plot, and this information is very professional and I would like to have any update about, thanks for sharing!!

kevin said...

Thanks. very helpful. if you are looking for something to do I could use some help please. I want to set it up so that it only matches if there are a certain amount of matches within subsections of a certain length i.e. split the string into substrings of say 9 and consider it a match only if 7 of these 9 are the same and consider this a match and print a dot. I'm aware of substr but I have failed in implementing it successfully. any help would be appreciated

Chetan said...

Hi Kevin
Thanks for visiting my blog. In this code, every character of the query sequence is matched with every character of the subject sequence. If the match is there a "." is printed else a blank " " is printed.

In your case, how about trying a for loop where you give the parametre of 7 and then implement the substring function.

mandar smart said...

thanks sir helped me a lot

Chetan said...

Mandar

I am glad that my blog could assist you in some manner. Hope to hear from you soon.

Ricardo I said...

Hi Mate,
Your link is broken...
I'm interested in, I hope you fix it soon...
Thank you...
R