Sequence landscape is a data structure that presents exact occurrences of substrings of a source string in a target string. It also specifies the frequency of each of these occurrences. The original construction algorithm [1] uses a directed acyclic word graph (DAWG), which is the smallest automaton that accepts all the substrings of a string, as the underlying data structure. Although the running time and space requirements for building the DAWG in asymptotically linear, the constants are relatively large.

Team

• Christina Boucher (PI)
• Basir Shariat
• Jaime Ruiz
• Narjes Sadat Movahedi Tabrizi
• Hamidreza Chitsaz
• Ross McConnell

Related Publications

HyDA-Vista: Towards Optimal Guided Selection of k-mer Size for Sequence Assembly
Basir Shariat, Narjes Sadat Movahedi, Hamidreza Chitsaz and Christina Boucher. To appear in BMC Bioinformatics

Downloads

SEQLandscape Generator

Computes the maximal sequence landscape of a target string with respect to some source string.

• README
• Source (v1)

SEQLandscape

An application that allow the visualiztion and exploration of a generated sequence landcape.
Requires Java

• Windown
• Mac OS X
• Linux