Software Open Access

SMRUCC/GCModeller alpha Release

谢桂纲; 關倩倩

GCModeller provides a set of .NET libraries and CLI tools for processing biological analysis data. Currently GCModeller can provides these productive ready libraries:

1.Basically libraries

  • NCBI data analysis toolkit: Genbank/Taxonomy/nt/nr database
  • Common Data: FastA database, FastQ, SAM data file I/O class
  • Biological Data Standard Supports: SBML(level 3), BIOM(level1), PSI, OBO
  • Biological Pathway Database: MetaCyc, Reactome, KEGG data tools for .NET language

2.Biological Data Visualization software API for .NET

  • Circos API(genomic visualizing), Cytoscape DataModel API(Biological network visualizing), SequenceLogo(Molecular motif site visualize)

3.Annotation Tools:

  • A complete NCBI localblast toolkit for proteins and nucleotide sequence analysis, includes parallel task library for Win/Linux Server and data analysis protocol.
  • SNP toolkit
  • Nucleotide sequence topology feature site analysis toolkit.
  • RegPrecise database tool and MEME software toolkit for the annotation of bacterial genomics regulation network.
  • Go(Gene Ontology) annotation tools

4.R language hybrids environment for bioinformatics

  • Includes basically R language API, and some R package API from CRAN and Bioconductor

5.WebAPI wrapper for KEGG database and RegPrecise Database

 

Publications

Here listing the scientific paperworks that based on the analysis services of GCModeller:

 

Niu, X.-N., et al. (2015). "Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola." BMC Microbiol 15(1): 1-15.

DOI: 10.1186/s12866-015-0562-x

Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid.

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  • Bland, C., et al. (2007). ""CRISPR recognition tool (CRT): a tool For automatic detection Of clustered regularly interspaced palindromic repeats."" BMC Bioinformatics 8: 209.

  • Caspi et al 2014, "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases," Nucleic Acids Research 42:D459-D471

  • David Croft, Antonio Fabregat Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani Garapati, Marc Gillespie, Maulik R. Kamdar, Bijay Jassal, Steven Jupe, Lisa Matthews, Bruce May, Stanislav Palatnik, Karen Rothfels, Veronica Shamovsky, Heeyeon Song, Mark Williams, Ewan Birney, Henning Hermjakob, Lincoln Stein, and Peter D'Eustachio The Reactome pathway knowledgebase Nucl. Acids Res. (1 January 2014) 42 (D1): D472-D477

  • Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645

  • Lim, K. and L. Wong (2014). ""Finding consistent disease subnetworks Using PFSNet."" Bioinformatics 30(2): 189-196.

  • RegPrecise 3.0 - A resource for genome-scale exploration of transcriptional regulation in bacteria. Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA. BMC Genomics. 2013 Nov 1;14:745

  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Research 2003 Nov; 13(11):2498-504

  • The MiST2 database: a comprehensive genomics resource on microbial signal transduction. Luke E. Ulrich and Igor B. Zhulin Nucleic Acids Research, 2010, doi:10.1093/nar/gkp940.

  • Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, "MEME SUITE: tools for motif discovery and searching", Nucleic Acids Research, 37:W202-W208, 2009.

  • Xie S, Shen B, Zhang C, Huang X * and Zhang Y *. sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PloS one, 2014

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Publication date:
October 10, 2016
DOI:
10.5281/zenodo.159947

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Keyword(s):
bacterial genomics annotation localblast pathway network Circos
Related identifiers:
Supplement to:
https://github.com/SMRUCC/GCModeller/tree/v0.0.1-alpha
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License (for files):
GNU General Public License v3.0 only

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