Online tool to design guideRNAs (sgRNAs) for CRISPR applications with microbes. Unlike most other CRISPR design tools, CRISPy-web allows the user to upload custom/non-model organisms genome data to screen for off-target effects. CRISPy-web can directly access antiSMASH results and use the antiSMAS-annotation to aid with the sgRNA design. CRISPy-web is based on CRISPy, a web-tool to find sgRNAs for Chinese hamster ovary (CHO-K1) cells.
- Ronda, C., et al., 2014, Biotechnol. Bioeng. 111:1604-16
- Blin, K., et al., 2016, Synth. Syst. Biotechnol., 10.1016/j.synbio.2016.01.003d
Interpro is a comprehensive resource on protein domains. The web tool InterProScan offers querying the Interpro database and identifying conserved protein domains in query sequences.
- Mitchell, A., et al., 2015, Nucleic Acids Res. 43:D213-21
- Jones, P., et al., 2014, Bioinformatics 30:1236-40
- Hunter, S., et al., 2009, Nucleic Acids Res. 37:D211-5
- Mulder, N. J. and Apweiler, R., 2008, Curr Protoc Bioinformatics Chapter 2:Unit 2 7
- Mulder, N. and Apweiler, R., 2007, Methods Mol. Biol. 396:59-70
The standalone tool MultiGeneBlast is a Blast extension that allows querying sequence databases with complete gene clusters / operons and thus allows the identification of similar pathways in other organisms.
Link for download:
User friendly GUI to the old, but very powerful PATSCAN utility, which is a powerful tool for pattern searching in DNA or amino acid sequences.
- PatScan: Dsouza, M., et al., 1997, Trends Genet. 13:497-8
- GUI: Blin et al., unpublished
- GUI: http://patscan.secondarymetabolites.org
- GUI source code: https://github.com/kblin/patscanui
- PatScan source code and documentation: http://blog.theseed.org/servers/2010/07/scan-for-matches.html