Everyone knows what DNA is these days. Hm. Just stumbled over today's article in Nature about Z-DNA and B-DNA with some nice pictures (see also the free Figure S8)
Frankly, I completely forgot about left-handed DNA. That brings me to a topic where I'm clearly lacking keywords: What is there on DNA apart from the raw sequence? I seems to be really similar to a normal cord. What can you do with a piece of cord? Similar things as with DNA. I remember...
that it has sometimes stuff attached to it (methylation),
that it is rolled into histones (chromatin structure),
that the direction of rotation sometimes changes (Z-DNA),
that it is sometimes easy to bend (flexibility),
that it can become strained (supercoiled),
Did I forget anything? (hope that there is no information encoded using knots)
I remember that at least for chromatin structure, z-dna and flexibility, there are predictions available somewhere on the Web, but I've never seen a genome browser that would display these features together... is there any integrated view of the DNA somewhere that would allow a global view of a given stretch of DNA? I mean, UCSC and Ensembl are putting loads of information everywhere imaginable... but nothing about stuff like this. Or do they?
Comments
well there's a project for you
Don't know if other people provide this kind of data in their browsers. However, it's certainly easy enough to add it yourself. Any "feature" (a region on a stretch of DNA with a start and an end) can be displayed. Typically you would (1) run the software that finds the feature, (2) write a parser to extract the coordinates and strand, (3) add that data to a file format such as GFF and (4) either upload to a browser website or install the browser yourself and load into a local database. All very easy using e.g. Bioperl, Bio::DB::GFF, MySQL and the Generic Genome Browser.
So there's a nice little bioinformatics project for you.