autometa is an automatic binning pipeline to obtain single genomes from metagenomic datasets
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- GUI: Blin et al., unpublished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