Using NCBIminer to search and download nucleotide sequences from GenBank

doi:10.17520/biods.2015120

Abstract

Abstract:

GenBank is the leading public genetic resources database and currently contains over 10¹² base pairs from about 300,000 formally described species. It offers valuable resources for studies on the evolution of species, genes, and genomes. However, difficulties in GenBank data mining hinder the potential wide application of this tool for big data collection. To address this issue, we introduce new bioinformatics software —NCBIminer. NCBIminer is a freely available, cross-platform, and user-friendly software for mining nucleotide sequences from GenBank. The main purpose of NCBIminer is to download sequences for user required genes and taxonomic groups based on gene names, types, and one or several reference sequences. The program algorithms have been described elsewhere and here, we focus on introducing the details in the usage of the program including how to install, run, and set parameters.

Key words: GenBank, bioinformatics, gene, phylogenetic evolution, DNA, nucleotide sequences

Xiaoting Xu, Zhiheng Wang, Dimitar Dimitrov, Carsten Rahbek. Using NCBIminer to search and download nucleotide sequences from GenBank[J]. Biodiv Sci, 2015, 23(4): 550-555.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2015120

https://www.biodiversity-science.net/EN/Y2015/V23/I4/550

Figures/Tables 2

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