Creating CpG dinucleotide map across a promoter
Posted 14 January 2005 - 08:03 PM
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.
Posted 15 January 2005 - 10:09 PM
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.
Posted 16 January 2005 - 02:42 PM
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.
Posted 16 January 2005 - 05:43 PM
Posted 16 January 2005 - 06:41 PM
pcrman, on Jan 16 2005, 06:43 PM, said:
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!
Posted 16 January 2005 - 08:45 PM
Posted 17 January 2005 - 07:53 PM