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-dimensio...

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Detalles Bibliográficos
Autores principales: Shen, Junjie, Zhang, Shuyu, Lee, Hoong-Chien, Hao, Bailin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2004
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172470/
https://www.ncbi.nlm.nih.gov/pubmed/15862120
http://dx.doi.org/10.1016/S1672-0229(04)02025-X
Descripción
Sumario: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.

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