ArticleBMC bioinformatics2010
DeltaProt: a software toolbox for comparative genomics.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- DWARF AND ROBUST PLANT regulates plant height via modulating gibberellin biosynthesis in chrysanthemum.Plant physiology · 2022Article
- Classification of Ankle Joint Stiffness during Walking to Determine the Use of Ankle Foot Orthosis after Stroke.Brain sciences · 2021Article
- Use of Raman spectroscopy to screen diabetes mellitus with machine learning tools.Biomedical optics express · 2018Article
- Altered Functional Connectivity Following an Inflammatory White Matter Injury in the Newborn Rat: A High Spatial and Temporal Resolution Intrinsic Optical Imaging Study.Frontiers in neuroscience · 2017Article
- A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule.BMC biology · 2016Article
- VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams.PloS one · 2016Article
- Imaging of an inflammatory injury in the newborn rat brain with photoacoustic tomography.PloS one · 2013Article
- Molecular characterization of cold adaptation of membrane proteins in the Vibrionaceae core-genome.PloS one · 2012Article
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3 authors.
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Abstract
backgroundStatistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, orthologous sequences from different habitats may be explored and compared. The main goal of the DeltaProt Toolbox is to provide users with important functionality that is needed for comparative screening and studies of extremophile proteins and protein classes. Visualization of the data sets is also the focus of this article, since visualizations can play a key role in making the various relationships transparent. This application paper is intended to inform the reader of the existence, functionality, and applicability of the toolbox.
resultsWe present the DeltaProt Toolbox, a software toolbox that may be useful in importing, analyzing and visualizing data from multiple alignments of proteins. The toolbox has been written in MATLAB™ to provide an easy and user-friendly platform, including a graphical user interface, while ensuring good numerical performance. Problems in genome biology may be easily stated thanks to a compact input format. The toolbox also offers the possibility of utilizing structural information from the SABLE or other structure predictors. Different sequence plots can then be viewed and compared in order to find their similarities and differences. Detailed statistics are also calculated during the procedure.
conclusionsThe DeltaProt package is open source and freely available for academic, non-commercial use. The latest version of DeltaProt can be obtained from http://services.cbu.uib.no/software/deltaprot/. The website also contains documentation, and the toolbox comes with real data sets that are intended for training in applying the models to carry out bioinformatical and statistical analyses of protein sequences.Equipped with the new algorithms proposed here, DeltaProt serves as an auxiliary analysis tool capable of visualizing and comparing orthologus protein sequences. The framework of the algorithms also enables easy incorporation of extra information on structure, if such data is available.
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