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