Xlandscape: the graphical display of word frequencies in sequences.

Abstract

To provide a graphical interface for the generation, display and manipulation of a sequence landscape that will run on all X-windows-based Unix workstations. The sequence landscape approach enables the representation of the frequency of occurrence of all query sequence sub-words within a database. The landscape approach can detect tandem and other repeating word motifs, specific sub-words that are over-represented words in a particular database using Markov probability and the preference for sub-words belonging to either one of two databases. All these features aid in the classification of a query sequence. Given the open-text format for sequences and databases, the Xlandscape tool can be applied to a wide range of problems.