Bioinformatics Functions

Here are links to various CGI/Perl functions I have written.

The main purpose of this page is to provide me with an easy access point for them

However, these also provide a view into my current thoughts and work in bioinformatics, both as research and as part of teaching in the NIU Bioinformatics Master's degree specialization.

Rick Johns July 24, 2001

e-mail:rjohns@niu.edu

Tandem Duplications working page (Dec 2004) here
Rice chromosome 10 BLAST dotplots (Jan 2004) here
Sample Annotation page here
Words found in rice gene annotations (April 2004) here
Large scale duplications on rice chromsome 10 (compared to Arabidopsis chr 1) (July 2002) here
Other rice info here
Gene Families: similar genes with and without introns in Arabidopsis here    Jan 25, 2002
PMBG talk 2002 here
Plant section talk December 2004 on tandem repeats here

Other people's pages

Chess Leslin here
Jennifer Bosch here
Chuck Leseberg here
Corey MacGregor here
My courses here

Older Stuff

Plot enzyme rate data Here
Find restriction sites
Similarity matrix and UPGMA tree of genetic marker data Here
Two dimensional plot of genetic marker data Here
Seedline clustering of genetic marker data Here
Retrieve DNA sequences from GenBank Here
Compare all Arabidopsis genes to other species with BLAST scores Here
Arabidopsis chromosome drawings: various scales Here
Words found in Arabidopsis annotation Here (Aug 2001)
Arabidopsis BLAST score vs. chromosome distance plots Here (Aug 2001)
ATG context: frequencies of bases around ATGs in Arabidopsis exons Here   Oct 2001
Find ESTs corresponding to Arabidopsis gene numbers and vice versa,
and whether they are on the AFGC and Affymetrix microarrays.		 here    March 5, 2002

Experimental Stuff--changes often, may not work

Arabidopsis repeat sequences plotted onto chromosomes Here
Link experimental chromosome image program Here
Link to all images for Arabidopsis DNA Dot plots Here
Test of GD graphics library here
Graph plot test here
JavaScript Test here