Short DNA and amino acid sequences (e.g. genes or proteins) have driven early bioinformatics research. Later, however, focus has shifted to more
sophisticated objects, such as various kinds of networks, and pure sequences
have taken a back seat.
The advent of a various high throughput sequencing technologies (aka "new generation sequencing") has given rise to new (or renewed) algorithmic challenges. It has also produced hundreds of complete genome and proteome sequences (with
thousands more in the making).
In addition to algorithmic questions, we also face many data discovery questions
that were inaccessible before. I will describe a number of approaches and results in this area.
* "biological sequences", of course (what did you have in mind?)