AIST > CBRC > SEQ > MCF

Talk slides

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 2012).
  • 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 University, 2011).
• A shorter talk (pdf) on sequence comparison that I gave at ISCB-Asia 2011, in Kuala Lumpur.
• An older lecture (pdf) on sequence comparison, with more algorithmic details (Kyoto University, 2008).

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 transitive overlaps.
• An idea for counting k-mers by sorting.
• 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).
• A 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