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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 (http://www.bcgsc.ca/platform/bioinfo/software/abyss) 1
AlignDNA a pairwise DNA alignment tool (http://www.geneinfinity.org/sms/sms_aligndna.html) 1
BLAST: Basic Local Alignment Search Tool a program that finds regions of local similarity between biological sequences (http://blast.ncbi.nlm.nih.gov) 7
CentroidFold a program that predicts an RNA secondary structure from an RNA sequence (http://www.ncrna.org/centroidfold) 1
CLC Genomics Workbench a comprehensive and user-friendly analysis package for analyzing, comparing, and visualizing next generation sequencing data (http://www.clcbio.com/products/clc-genomics-workbench) 5
CodonCode Aligner a program for sequence assembly, contig editing, and mutation detection (http://www.codoncode.com/aligner) 1
Cytoscape an open source software platform for visualizing and integrating complex networks (http://www.cytoscape.org) 1
FastPCR a program for PCR primer design (http://en.bio-soft.net/pcr/FastPCR.html) 1
Gene Construction Kit a program for plasmid mapping (http://www.textco.com/gene-construction-kit.php) 1
Geneious a program for handling and managing bioinformatics data (http://www.geneious.com) 7
Gibthon Ligation Calculator a software tool for calculating reactant concentrations for DNA ligation (http://django.gibthon.org/tools/ligcalc) 1
JWS online a tool for simulation of kinetic models from a curated model database (http://jjj.biochem.sun.ac.za) 1
Lasergene-DNAStar comprehensive software for DNA and protein sequence analysis, contig assembly and sequence project management (http://www.dnastar.com) 7
Mascot a search engine which uses mass spectrometry data to identify proteins from primary sequence databases (http://www.matrixscience.com/search_intro.html) 1
Mauve a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion (http://gel.ahabs.wisc.edu/mauve) 1
Merlin a M.A.G.E. optimization tool developed by the Cross-disciplinary Integration of Design Automation Research group at Boston University (http://cidar1.bu.edu:8080) 1
OligoAnalyzer software for comprehensive oligonucleotide analysis (http://www.idtdna.com/analyzer/Applications/OligoAnalyzer) 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 (http://www.ncbi.nlm.nih.gov/projects/gorf) 1
PaR-PaR software that allows researchers to use liquid-handling robots effectively (http://prpr.jbei.org) 1
Pigeon Synthetic Biology Open Language picture generator (http://cidar1.bu.edu:5801/pigeon1.php) 1
PlasMapper software that automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input (http://wishart.biology.ualberta.ca/PlasMapper) 1
PyMOL a user-sponsored molecular visualization system for rendering and animating 3D molecular structures on an open-source foundation (http://pymol.org) 1
RNAstructure a complete package for RNA and DNA secondary structure prediction and analysis (http://rna.urmc.rochester.edu/RNAstructure.html) 1
Serial Cloner freeware with an intuitive interface that assists in DNA cloning, sequence analysis and visualization (http://serialbasics.free.fr/Serial_Cloner.html) 3
Sequencher DNA sequencing software (http://genecodes.com/sequencher-features) 1
SSC: Stochastic Simulation Compiler a tool for creating exact stochastic simulations of biochemical reaction networks (http://web.mit.edu/irc/ssc) 1
SWISS-PDB viewer (aka DeepView) an application that provides a user friendly interface allowing analysis of several proteins at the same time (http://spdbv.vital-it.ch) 1
Synbiota a platform of collaborative services to design, store, post, organize, access, or share information (https://mozillalabs.com/en-US/synbiota) 2
Velvet a set of algorithms to manipulate de Bruijn graphs for genomic sequence assembly (http://www.ebi.ac.uk/~zerbino/velvet) 1