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...

Descripción completa

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
_version_ 1782484134142148608
author Shen, Junjie
Zhang, Shuyu
Lee, Hoong-Chien
Hao, Bailin
author_facet Shen, Junjie
Zhang, Shuyu
Lee, Hoong-Chien
Hao, Bailin
author_sort Shen, Junjie
collection PubMed
description 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.
format Online
Article
Text
id pubmed-5172470
institution National Center for Biotechnology Information
language English
publishDate 2004
publisher Elsevier
record_format MEDLINE/PubMed
spelling pubmed-51724702016-12-23 SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts Shen, Junjie Zhang, Shuyu Lee, Hoong-Chien Hao, Bailin Genomics Proteomics Bioinformatics Method 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. Elsevier 2004-08 2016-11-28 /pmc/articles/PMC5172470/ /pubmed/15862120 http://dx.doi.org/10.1016/S1672-0229(04)02025-X Text en . http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Method
Shen, Junjie
Zhang, Shuyu
Lee, Hoong-Chien
Hao, Bailin
SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts
title SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts
title_full SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts
title_fullStr SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts
title_full_unstemmed SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts
title_short SeeDNA: A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts
title_sort seedna: a visualization tool for k-string content of long dna sequences and their randomized counterparts
topic Method
url 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
work_keys_str_mv AT shenjunjie seednaavisualizationtoolforkstringcontentoflongdnasequencesandtheirrandomizedcounterparts
AT zhangshuyu seednaavisualizationtoolforkstringcontentoflongdnasequencesandtheirrandomizedcounterparts
AT leehoongchien seednaavisualizationtoolforkstringcontentoflongdnasequencesandtheirrandomizedcounterparts
AT haobailin seednaavisualizationtoolforkstringcontentoflongdnasequencesandtheirrandomizedcounterparts

Ejemplares similares