What tools are available for determining patterns in short, semi-random sequences of variables? [more inside]
I'm a final year biochemistry undergrad, and through my internships / reading of papers / etc, I've become keenly aware that I'd like to be more conversant with computer science approaches to the field. The sheer volume of approaches and strategies in bioinformatics is a little overwhelming, though: where's a good place to start focusing my attention? I have strong maths skills, but my programming ability is limited to pecking out simple instruction sets in Python or Matlab, and my research work thus far has mostly been on isolating and characterising protein markers from serum / urine / etc.
How can I generate a dotplot of general files? [more inside]
I'd like to learn about SVM, HMM and wavelet algorithms in their usage in bioinformatics. I have a somewhat rudimentary understanding of the underlying mathematics from Wikipedia and a couple other sources, but I find that a concrete demonstration of their application fleshes it out. Are there texts, software packages (preferably free) or papers you'd recommend that: 1) includes good starter problem sets, or; 2) demonstrates how these techniques are used in research applications (beyond "we used xyz here"). Thanks!
How do cells form various shapes? [more inside]