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BME 110L / BIOL 181L Computational Biology Tools

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

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BME 110L / BIOL 181L Computational Biology Tools

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  1. 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

  2. BME 110L / BIOL 181L A question that came up: What is the difference between a chromosome and a plasmid (both are circular in D.radiodurans)? •

  3. BME 110L / BIOL 181L A question that came up: What is the difference between a contig and a scaffold (both used in genomic sequencing)?

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

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