BME 110L / BIOL 181L

Computational Biology Tools

www.soe.ucsc.edu/classes/bme110/Winter09

January 22: • A few tidbits that came up

- chromosome versus plasmid in bacteria- “contig”, “scaffold” - genomics terminology

• More sequence comparison - large genome fragments (pair-wise): Dotplots - even more sensitive than BLASTP: PSI-BLAST

(Slides by Prof. Todd Lowe).

• In-class demo/exercise: PSI-BLAST/Dotlet+JDotter

Evening Section: HW2 is available via course calendar

Accompanying Reading (B4D): Chp 8; NCBI-BLAST tutorial

BME 110L / BIOL 181L

A question that came up:What is the difference between a chromosomeand a plasmid (both are circular in D.radiodurans)?

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BME 110L / BIOL 181L

A question that came up: What is the difference between a contig and a scaffold (both used in genomic sequencing)?

From Zivanovic et al., NAR 30: 1902-10 (2002).