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 |