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lecture_notes:05-10-2010

SSAKE assembly

John Kim demonstrated the results obtained from SSAKE assembly on POG.

  • SSAKE is a short read De novo assembly program.
  • Came out only when Solexa had short reads.
  • Algorithm needs ~25mer perfect error free reads.
  • Basically requires dataset to be perfect.
  • SSAKE is an example of consensus overlapping.
  • Hashes the reads, where sequence is the key, and the number of occurrences of the sequence constitutes value.
  • Has memory issues.
  • Builds prefix tree of all the overlaps, until all the reads have exact overlap with the seed.
  • It is a greedy algorithm.
  • SSAKE when applied on POG mate-paired data, the data was trimmed and translated.
  • This algorithm is not much useful as it produces very poor results.
  • Not a good assembler for Banana Slug genome.

Slug Locomotion

Jenny talked about the mechanism behind Banana Slug locomotion.

  • The entire bottom of slug is its foot.
  • It moves along the whole length of foot creating muscular wave.
  • The surface of the slug has sticky mucus which assists their movement.
  • The motion flow is referred to as : Non-Newtonian flow.
  • Retrograde motion, where waves go backward and slug moves forward.
  • Speed of wave is proportional to speed of slugs. It has been determined that wave is 3.3 faster than slug motion.
  • Interwave - where a muscle relaxes and stretches.
  • At MIT robo-slugs are developed to study the mechanism behind slug locomotion.
  • For mucus they mix laponite (a kind of clay) in water.
  • The basic mechanism behind slug locomotion is : slide → stick → pull.
  • slugs can move only with mucus.
  • Studies are done to see what happens when mucus dries.
  • The mucus layer is thin, has the property of suction.
  • 30% of energy required for locomotion is spent on making glycoprotein, 10% on the muscular motion, and the rest on the inefficiency of motion.
  • Several studies are done on stress vs strain rate.
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lecture_notes/05-10-2010.txt · Last modified: 2010/05/16 22:48 by jstjohn