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Creating CpG dinucleotide map across a promoter


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#1 methylnick

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Posted 14 January 2005 - 08:03 PM

Hi,

I have been performing a large number of bisulfite sequencing assays. I have a fasta file of all the sequences I have looked at. I was wondering if anyone knows of a program than can read these sequences and give a postscript or similar output file of the exact positions of CpG or any other dinucleotide. I am after a positional plot and *NOT* a dinucleotide composition plot.

For example the plots of CpG and GpC positions as published in the classic Gardiner-Garden and Frommer paper in 1987.

Cheers!

Nick

#2 pcrman

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Posted 15 January 2005 - 10:09 PM

Hi Nick,

To my best knowledge, there is no such program that can do this. Although some sequence alignment programs such as Vector NIT can help, I prefer manually checking the sequences. I don't know if your sequences are from direct sequencing or cloning. For direct sequencing, you definitely need manual analysis. Recently I have sequenced near 1000 clones and just printed out the chromagraph, checked one by one and recorded the results in a spread sheet.

#3 methylnick

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Posted 16 January 2005 - 02:42 PM

Hi PCRman,

That is what I have been doing also. I have been using the staden package for viewing my chromatographs. It is a very laborious task!

What I was after was a program that could map the position of CpG sites within a region of interest prior to bisulfite modification so I can get a scale map of CG positions within the promoter and maybe also GC positions as well.

Cheers

Nick

#4 pcrman

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Posted 16 January 2005 - 05:43 PM

I see. Actually you want to plot the postions of CpGs from a sequence not analyzing the results of bisulfite sequencing. I don't know if you have used MethPrimer program whick can plots CpGs on the input seqeunce but not GCs. CpG island Searcher can also do that. You can find those programs in this thread: http://www.protocol-...?showtopic=4589

#5 methylnick

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Posted 16 January 2005 - 06:41 PM

I see. Actually you want to plot the postions of CpGs from a sequence not analyzing the results of bisulfite sequencing. I don't know if you have used MethPrimer program whick can plots CpGs on the input seqeunce but not GCs. CpG island Searcher can also do that. You can find those programs in this thread: http://www.protocol-...?showtopic=4589

A ha!

yes that is what I am after! I might get in touch with the authors about what I would like specifically, because I have over 200 regions of interest that I have studied and would like to display each graphically for my thesis!

Cheers PCRman

Nick

#6 pcrman

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Posted 16 January 2005 - 08:45 PM

If you know a little bit of perl, you can do it yourself. Bioperl has a module for drawing graph.

#7 methylnick

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Posted 17 January 2005 - 07:53 PM

Checking out some sites on how to use perl at the moment,

cheers!

Nick

#8 pcrman

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Posted 18 January 2005 - 09:59 AM

If you want to DIY, use the GD library http://stein.cshl.org/WWW/software/GD/. It is not very hard and is fun to play with it.

#9 methylnick

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Posted 18 January 2005 - 07:28 PM

Cool I will look into it.

cheers pcrman




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