I181 V2000 Assignment 7 - Applications of search in bioinformatics Searching in Fasta. Step 3 of Fasta is to combine good diagonal runs of hits. This can be done by representing the runs and their relationships in a graph where each node is a run and where there is a directed edge from one run to another if the first run's end precedes the start of the second run. The figure below shows a graph representation. The nodes are numbered in accordance with the figure above.
Red numbers are weights of nodes, blue numbers are edge weights.
Finding the longest commom substring using a search. We have earlier looked at methods for comparing two strings. One way to compare more than two strings is to look for patterns common to the strings. The simplest form of patterns that are used are the so-called substring patterns. A string S matches a pattern P if it contains P as a substring.