SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts
- Author:
Shen JUNJIE
1
;
Zhang SHUYU
;
Lee HOONG-CHIEN
;
Hao BAILIN
Author Information
1. 浙江大学
- Keywords:
K-tuple;
visualization;
palindrome;
randomized sequence
- From:
Genomics, Proteomics & Bioinformatics
2004;2(3):192-196
- CountryChina
- Language:Chinese
-
Abstract:
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.
