BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S -Locus

AbstractNowadays, bioinformatics is one of the most important areas in modern biology and the creation of high-quality scientific software supporting this recent research area is one of the core activities of many researchers. In this context, high-quality sequence datasets are needed to perform inferences on the evolution of species, genes, and gene families, or to get evidence for adaptive amino acid evolution, among others. Nevertheless, sequence data are very often spread over several databases, many useful genomes and transcriptomes are non-annotated, the available annotation is not for the desired coding sequence isoform, and/or is unlikely to be accurate. Moreover, although the FASTA text-based format is quite simple and usable by most software applications, there are a number of issues that may be critical depending on the software used to analyse such files. Therefore, researchers without training in informatics often use a fraction of all available data. The above issues can be addressed using already available software applications, but there is no easy-to-use single piece of software that allows performing all these tasks within the same graphical interface, such as the one here presented, named BDBM (Blast DataBase Manager). BDBM can be used to efficiently get gene sequences from annotated and non-annotated genomes and transcriptomes. Moreover, it can be used to look for alternatives to existing annotations and to easily create reliable custom databases. Such dat...
Source: Interdisciplinary Sciences, Computational Life Sciences - Category: Bioinformatics Source Type: research

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Source: Canadian Journal of Urology - Category: Urology & Nephrology Tags: Can J Urol Source Type: research
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Source: Canadian Journal of Urology - Category: Urology & Nephrology Tags: Can J Urol Source Type: research
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Source: Canadian Journal of Urology - Category: Urology & Nephrology Tags: Can J Urol Source Type: research
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Source: Canadian Journal of Urology - Category: Urology & Nephrology Tags: Can J Urol Source Type: research
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Source: RSC - Organic and Biomolecular Chemistry - Category: Molecular Biology Authors: Source Type: research
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Source: RSC - Organic and Biomolecular Chemistry - Category: Molecular Biology Authors: Source Type: research
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Source: Global Health Action - Category: International Medicine & Public Health Tags: Glob Health Action Source Type: research
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Source: Pathogens and Global Health - Category: International Medicine & Public Health Tags: Pathog Glob Health Source Type: research
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Source: AllAfrica News: Health and Medicine - Category: African Health Source Type: news
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