27 April 2010


Just a little dump of some old stuff from my previous website. Enjoy!

I have been interested for some time in the field of Bioinformatics. On this page are a few of my modest contributions to the field. They are free for use in your research - all I ask is a citation. I'm currently working on a JAVA program to store and analyse genotypic information, and to parse SNP files. Hence the name ParSNiP. It has so far been programmed by Dr Charles Philpott, but I'm hoping to add a few more tweaks before making it generally available.

CALLELE (plus associated files)

A little program I wrote to convert non-integer allele sizes (such as the output from GenoTyper) into numbered alleles for direct use in LINKAGE software. It will allow you to totally slash the time it takes to analyse your linkage data. Using CALLELE, I can get from an allele table in GenoTyper to a LOD score in about 5 seconds. Contact me by leaving a comment on this thread, and I'll send you the code. It is neither big nor clever...


Not a program, but a format for the depiction of genetic pedigree data using standard ASCII text characters.

[_] Joe Bloggs Senior
(#) | Mary Bloggs
|-[#] Joe Bloggs Junior
|-(_) Shirley Bloggs

Basically, you use a proportional font (like Courier), and turn the pedigree on its side. Use square brackets [_] for a male, round brackets (_) for a female, and greater/less than signs <_> for sex-unknown. Put an underscore between the brackets for unaffected, and whatever you want (like a hash #) for affected. Each individual has his/her own line, and in general, older people are higher up than younger people (and younger generations are further to the right). You get the general idea?

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