Marchywka files at phluant.com
Idiosyncratic NCBI eutils bash script: eutilsnew.zip
Sample alignment/annotation file from mm_align_tool : qseg.bmp
Sample graphic of TLR-3 hits, unaligned but marked with prosite rules
R scatter plot of ecoli alignment features, partial filter
A few excerpts from the html annotater with PROSITE coloring.
More examples, consistent coloring of RCAN exons.
The pseudoknot overlay