AIST > CBRC > SEQ > MCF
These talks have a lot of overlap, but there are some
differences between them as well.
- An educational lecture (pdf) on
finding and aligning related sequences (BioInfoSummer, University of
Adelaide, Dec 2012).
- A 4½ hour (!) introductory talk and tutorial (pdf) on "Prediction of homology between biological sequences" (Ochanomizu University, Oct 2012).
- A talk (pdf) on statistical
models for various types of sequence comparison (Tokyo, Oct
- With an embarrassing "Smith-Waterman-Gotoh-Frith" algorithm,
which I now realize is similar to the "repeated matches" algorithm
in the Durbin et al. textbook.
- A more-educational lecture
(pdf) on sequence comparison (Tokyo University, Jun 2012).
- A more-research lecture (pdf) that
describes my recent interests in sequence comparison (Tokyo
- A shorter talk (pdf) on
sequence comparison that I gave at ISCB-Asia 2011, in Kuala
- An older lecture (pdf) on sequence
comparison, with more algorithmic details (Kyoto University,
Notes & ideas
These are thoughts that I'm sharing with the world, so they have
more chance of being useful.
- A note (pdf) on applying
hidden Markov models to uncertain (fastq) sequences.
- An idea for genome assembly by radix
sort (pdf), with some thoughts on dealing with contained reads and
- An idea for counting k-mers by
- A technical note (pdf) on split
alignment, where different parts of one query sequence may match
disjoint parts of a genome.
- A technical note (pdf) on affine-gap
alignment and pair HMMs (Apr 2012).
- A technical note (pdf) on aligning
paired DNA reads to a genome (Feb 2011).
technical note (pdf) on aligning color
sequences to DNA sequences (Dec 2010).
- A journal club review of "Compressed
indexing and local alignment of DNA" (Jan 2009).
Last modified 2012-12-13