Literature DB >> 33552037

BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts.

Beibei Wang1,2, Huayi Yang1, Jianan Sun1, Chuhao Dou1, Jian Huang1,2, Feng-Biao Guo1,2.   

Abstract

Synthetic biology seeks to create new biological parts, devices, and systems, and to reconfigure existing natural biological systems for custom-designed purposes. The standardized BioBrick parts are the foundation of synthetic biology. The incomplete and flawed metadata of BioBrick parts, however, are a major obstacle for designing genetic circuit easily, quickly, and accurately. Here, a database termed BioMaster http://www.biomaster-uestc.cn was developed to extensively complement information about BioBrick parts, which includes 47,934 items of BioBrick parts from the international Genetically Engineered Machine (iGEM) Registry with more comprehensive information integrated from 10 databases, providing corresponding information about functions, activities, interactions, and related literature. Moreover, BioMaster is also a user-friendly platform for retrieval and analyses of relevant information on BioBrick parts.
Copyright © 2021 Wang, Yang, Sun, Dou, Huang and Guo.

Entities:  

Keywords:  BioBrick parts; database integration; genetic circuit design; iGEM Registry; synthetic biology

Year:  2021        PMID: 33552037      PMCID: PMC7858672          DOI: 10.3389/fmicb.2021.593979

Source DB:  PubMed          Journal:  Front Microbiol        ISSN: 1664-302X            Impact factor:   5.640


  38 in total

1.  Standard virtual biological parts: a repository of modular modeling components for synthetic biology.

Authors:  M T Cooling; V Rouilly; G Misirli; J Lawson; T Yu; J Hallinan; A Wipat
Journal:  Bioinformatics       Date:  2010-02-16       Impact factor: 6.937

2.  Building outside of the box: iGEM and the BioBricks Foundation.

Authors:  Christina D Smolke
Journal:  Nat Biotechnol       Date:  2009-12       Impact factor: 54.908

Review 3.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

4.  Genetic circuit design automation.

Authors:  Alec A K Nielsen; Bryan S Der; Jonghyeon Shin; Prashant Vaidyanathan; Vanya Paralanov; Elizabeth A Strychalski; David Ross; Douglas Densmore; Christopher A Voigt
Journal:  Science       Date:  2016-04-01       Impact factor: 47.728

5.  KEGG: new perspectives on genomes, pathways, diseases and drugs.

Authors:  Minoru Kanehisa; Miho Furumichi; Mao Tanabe; Yoko Sato; Kanae Morishima
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

6.  Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks.

Authors:  Ramzan Kh Umarov; Victor V Solovyev
Journal:  PLoS One       Date:  2017-02-03       Impact factor: 3.240

7.  The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Authors:  Damian Szklarczyk; John H Morris; Helen Cook; Michael Kuhn; Stefan Wyder; Milan Simonovic; Alberto Santos; Nadezhda T Doncheva; Alexander Roth; Peer Bork; Lars J Jensen; Christian von Mering
Journal:  Nucleic Acids Res       Date:  2016-10-18       Impact factor: 16.971

8.  UniProt: the universal protein knowledgebase.

Authors: 
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

9.  ExplorEnz: the primary source of the IUBMB enzyme list.

Authors:  Andrew G McDonald; Sinéad Boyce; Keith F Tipton
Journal:  Nucleic Acids Res       Date:  2008-09-06       Impact factor: 16.971

10.  A one pot, one step, precision cloning method with high throughput capability.

Authors:  Carola Engler; Romy Kandzia; Sylvestre Marillonnet
Journal:  PLoS One       Date:  2008-11-05       Impact factor: 3.240

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