Banana Slug Genomics

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====== 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.
Banana Slug Genomics

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