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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, how do they move? * 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 Stanford 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/05-10-2010.1273648194.txt.gz · Last modified: 2010/05/12 07:09 by svasili