SeeDNA: a visualization tool for K-string content of long DNA sequences and their randomized counterparts.
An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK+ support. It displays two-dimensional (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/or its randomized counterpart. It is also capable of showing the difference of K-string distributions between two sequences. The C source code using the GTK+ package is freely available.
Shen
Junjie
J
Department of Computer Science, Zhejiang University, Hangzhou 310027, China.
Zhang
Shuyu
S
Lee
Hoong-Chien
HC
Hao
Bailin
B
D000465:Algorithms; D001482:Base Composition; D001483:Base Sequence / Q000235:genetics*; D003196:Computer Graphics; D023281:Genomics / Q000379:methods*; D012984:Software; D014584:User-Computer Interface