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C-mii: a tool for plant miRNA and target identification

BACKGROUND: MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have spe...

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Autores principales: Numnark, Somrak, Mhuantong, Wuttichai, Ingsriswang, Supawadee, Wichadakul, Duangdao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521235/
https://www.ncbi.nlm.nih.gov/pubmed/23281648
http://dx.doi.org/10.1186/1471-2164-13-S7-S16
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author Numnark, Somrak
Mhuantong, Wuttichai
Ingsriswang, Supawadee
Wichadakul, Duangdao
author_facet Numnark, Somrak
Mhuantong, Wuttichai
Ingsriswang, Supawadee
Wichadakul, Duangdao
author_sort Numnark, Somrak
collection PubMed
description BACKGROUND: MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. RESULTS: To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. CONCLUSIONS: C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms.
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spelling pubmed-35212352012-12-14 C-mii: a tool for plant miRNA and target identification Numnark, Somrak Mhuantong, Wuttichai Ingsriswang, Supawadee Wichadakul, Duangdao BMC Genomics Proceedings BACKGROUND: MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. RESULTS: To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. CONCLUSIONS: C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms. BioMed Central 2012-12-07 /pmc/articles/PMC3521235/ /pubmed/23281648 http://dx.doi.org/10.1186/1471-2164-13-S7-S16 Text en Copyright ©2012 Numnark et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Numnark, Somrak
Mhuantong, Wuttichai
Ingsriswang, Supawadee
Wichadakul, Duangdao
C-mii: a tool for plant miRNA and target identification
title C-mii: a tool for plant miRNA and target identification
title_full C-mii: a tool for plant miRNA and target identification
title_fullStr C-mii: a tool for plant miRNA and target identification
title_full_unstemmed C-mii: a tool for plant miRNA and target identification
title_short C-mii: a tool for plant miRNA and target identification
title_sort c-mii: a tool for plant mirna and target identification
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521235/
https://www.ncbi.nlm.nih.gov/pubmed/23281648
http://dx.doi.org/10.1186/1471-2164-13-S7-S16
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