Tag: Construction

GEDpm-cg – Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum

GEDpm-cg

:: DESCRIPTION

GEDpm-cg enables users to perform the efficient, automated and high-throughput design of single nucleotide editing in C. glutamicum chromosome. The counter-selection HR system and the overlap-based assembly method were chosen as the loading techniques. Homologous arms and primers required for genetic modification, vector DNA assembly and sequencing verification were provided as design results.

::DEVELOPER

Biodesign Centre, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server
  • Python

:: DOWNLOAD

GEDpm-cg

:: MORE INFORMATION

Citation

Yang Y, Mao Y, Liu Y, Wang R, Lu H, Li H, Luo J, Wang M, Liao X, Ma H.
GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum.
Front Bioeng Biotechnol. 2021 Oct 15;9:768289. doi: 10.3389/fbioe.2021.768289. PMID: 34722482; PMCID: PMC8554027.

Rainbow beta 1.2 – Toolbox for Phylogenetic Supertree Construction & Analysis

Rainbow beta 1.2

:: DESCRIPTION

Rainbow is a program that provides a graphic user interface to construct supertrees using different methods. It also provides tools to analyze the quality of the supertrees produced.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science , Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Rainbow

:: MORE INFORMATION

Citation

D. Chen, O. Eulenstein and D. Fernández-Baca
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Bioinformatics (2004) 20 (16): 2872-2873.

Customprodbj v1.2.0 – Customized Protein Database Construction

Customprodbj v1.2.0

:: DESCRIPTION

Customprodbj is a Java-based tool for customized protein database construction. It can be used to (1) build a customized database based on single VCF file, (2) build a customized database based on multiple VCF files from a sample and (3) build a customized database based on multiple VCF files from multiple samples.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

Customprodbj

:: MORE INFORMATION

EFFECT 2013 – Automated Construction and Extraction of Features for Classification of Biological Sequences

EFFECT 2013

:: DESCRIPTION

EFFECT is an algorithmic framework for automated detection of functional signals in biological sequences.

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • BioJava

:: DOWNLOAD

 EFFECT

:: MORE INFORMATION

Citation

Kamath U, De Jong K, Shehu A.
Effective automated feature construction and selection for classification of biological sequences.
PLoS One. 2014 Jul 17;9(7):e99982. doi: 10.1371/journal.pone.0099982. PMID: 25033270; PMCID: PMC4102475.

IPATHCONS 1.0.6 – Insect Pathway Construction tool

IPATHCONS 1.0.6

:: DESCRIPTION

iPathCons is a tool for knowledge-based construction of pathways from the transcriptomes or the official gene sets of genomes.

::DEVELOPER

Li Lab: Insect Genomic and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IPATHCONS

:: MORE INFORMATION

Citation

iPathCons and iPathDB: an improved insect pathway construction tool and the database.
Zhang Z, Yin C, Liu Y, Jie W, Lei W, Li F.
Database (Oxford). 2014 Nov 11;2014. pii: bau105. doi: 10.1093/database/bau105.

MC-NET 1.0 – Construction of Phylogenetic Networks

MC-NET 1.0

:: DESCRIPTION

MC-Net is A method for the construction of phylogenetic networks based on Monte-Carlo method

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

 MC-NET

:: MORE INFORMATION

Citation

BMC Evol Biol. 2010 Aug 20;10:254. doi: 10.1186/1471-2148-10-254.
MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method.
Eslahchi C1, Habibi M, Hassanzadeh R, Mottaghi E.

Tripal 7.x-3.6 – Construction of online Genetic and Genomic databases

Tripal 7.x-3.6

:: DESCRIPTION

Tripal is a collection of open-source freely available Drupal modules and is a member of the GMOD family of tools. Tripal serves as a web interface for the GMOD Chado database and is designed to allow anyone with genomic data to quickly create an online genomic database using community supported tools.

::DEVELOPER

Tripal team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • PHP
  • phpPgAdmin
  • MySQL or PostgreSQL
  • Chado

:: DOWNLOAD

 Tripal

:: MORE INFORMATION

Citation

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.
Sanderson LA, Ficklin SP, Cheng CH, Jung S, Feltus FA, Bett KE, Main D.
Database (Oxford). 2013 Oct 25;2013:bat075. doi: 10.1093/database/bat075.

stringgaussnet 1.1 – PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor

stringgaussnet 1.1

:: DESCRIPTION

stringgaussnet is a toolbox for a construction of protein-protein interaction networks through the ‘STRING’ application programming interface, and an inference of Gaussian networks through ‘SIMoNe’ and ‘WGCNA’ approach, from DE genes analysis results and expression data. Additional functions are provided to import automatically networks into an active ‘Cytoscape’ session.

::DEVELOPER

Emmanuel Chaplais <emmanuel.chaplais at inserm.fr>, Henri-Jean Garchon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R

:: DOWNLOAD

 stringgaussnet

:: MORE INFORMATION

Citation

stringgaussnet: from differentially expressed genes to semantic and gaussian networks generation.
Chaplais E, Garchon HJ.
Bioinformatics. 2015 Jul 30. pii: btv450.

HighMap – Construction and Analysis of High-density Linkage Map

HighMap

:: DESCRIPTION

HighMap software is suitable for genetic map. This software utilized maximum likelihood and smooth algorithm, and could deal with ten thousand markers that make map distance more stably.

::DEVELOPER

Biomarker Technologies Corporation

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Construction and analysis of high-density linkage map using high-throughput sequencing data.
Liu D, Ma C, Hong W, Huang L, Liu M, Liu H, Zeng H, Deng D, Xin H, Song J, Xu C, Sun X, Hou X, Wang X, Zheng H.
PLoS One. 2014 Jun 6;9(6):e98855. doi: 10.1371/journal.pone.0098855.

ParaBWT 1.0.8 – Parallel Burrows Wheeler Transform Construction

ParaBWT 1.0.8

:: DESCRIPTION

ParaBWT is a new and practical parallelized Burrows-Wheeler transform (BWT) and suffix array construction algorithm for big genome data, which has a linear space complexity with a small constant factor.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ParaBWT 

:: MORE INFORMATION

Citation:

Liu Y, Hankeln T, Schmidt B.
Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data.
IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun;13(3):592-8. doi: 10.1109/TCBB.2015.2430314. PMID: 27295644.