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Table 4 Additional software tools used for synthetic biology research by survey participants

From: A survey of enabling technologies in synthetic biology

Software tool Description (URL) N
ABySS: Assembly By Short Sequences a de novo, parallel, paired-end sequence assembler that is designed for short reads ( 1
AlignDNA a pairwise DNA alignment tool ( 1
BLAST: Basic Local Alignment Search Tool a program that finds regions of local similarity between biological sequences ( 7
CentroidFold a program that predicts an RNA secondary structure from an RNA sequence ( 1
CLC Genomics Workbench a comprehensive and user-friendly analysis package for analyzing, comparing, and visualizing next generation sequencing data ( 5
CodonCode Aligner a program for sequence assembly, contig editing, and mutation detection ( 1
Cytoscape an open source software platform for visualizing and integrating complex networks ( 1
FastPCR a program for PCR primer design ( 1
Gene Construction Kit a program for plasmid mapping ( 1
Geneious a program for handling and managing bioinformatics data ( 7
Gibthon Ligation Calculator a software tool for calculating reactant concentrations for DNA ligation ( 1
JWS online a tool for simulation of kinetic models from a curated model database ( 1
Lasergene-DNAStar comprehensive software for DNA and protein sequence analysis, contig assembly and sequence project management ( 7
Mascot a search engine which uses mass spectrometry data to identify proteins from primary sequence databases ( 1
Mauve a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion ( 1
Merlin a M.A.G.E. optimization tool developed by the Cross-disciplinary Integration of Design Automation Research group at Boston University ( 1
OligoAnalyzer software for comprehensive oligonucleotide analysis ( 1
ORF Finder: Open Reading Frame Finder a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user’s sequence or in a sequence already in the database ( 1
PaR-PaR software that allows researchers to use liquid-handling robots effectively ( 1
Pigeon Synthetic Biology Open Language picture generator ( 1
PlasMapper software that automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input ( 1
PyMOL a user-sponsored molecular visualization system for rendering and animating 3D molecular structures on an open-source foundation ( 1
RNAstructure a complete package for RNA and DNA secondary structure prediction and analysis ( 1
Serial Cloner freeware with an intuitive interface that assists in DNA cloning, sequence analysis and visualization ( 3
Sequencher DNA sequencing software ( 1
SSC: Stochastic Simulation Compiler a tool for creating exact stochastic simulations of biochemical reaction networks ( 1
SWISS-PDB viewer (aka DeepView) an application that provides a user friendly interface allowing analysis of several proteins at the same time ( 1
Synbiota a platform of collaborative services to design, store, post, organize, access, or share information ( 2
Velvet a set of algorithms to manipulate de Bruijn graphs for genomic sequence assembly ( 1