Computational Biology Scribe Notes for Class 20
June 19, 2000

Scribe: J. Zwolak

The Shortest Common Superstring can be used in fragment assembly in Biology. However there are some problems that arise by using a simple straight forward SCS algorithm.
GREEDY --- Take the two strings with the greatest overlap. Combine them and repeat the process until one string is left. This algorithm is a simple SCS approximation.
MGREEDY --- Create an overlap graph. Partition the graph into cycles. Concatenate the SCS of each cycle (this was not clear to me, but this is how I understand it).
TGREEDY --- Run MGREEDY then GREEDY. Gives the best approximation to SCS.
To address some of the problems with the input fragments (ie reverse compliments and errors) the compliments of the fragments can be included in the list of fragments and/or errors can be permitted in the overlap.

Please report any problems found in these pages to:

CS6104 Account (cs6104@courses.cs.vt.edu)