GBioinformatics tools

Essential Bioinformatics Web Services (EBWS)

Nine tools for everyday DNA, RNA and protein work. Described in Kaloudas, Pavlova and Penchovsky, IEEE/ACM TCBB (2019), funded by BNSF grant DN13/14/20.12.2017.

• Reverse complement (RevComOligo)Reverse complementary strand of a DNA sequence.
• Random oligomer generatorRandom DNA, RNA or peptide sequences of a set length.
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  Motif finderFind motifs in DNA, RNA or protein, with wildcards and IUB codes.
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  Restriction mappingRestriction sites for 1,502 enzymes, or digestion with chosen enzymes.
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  Prokaryotic ORF finderOpen reading frames and promoter boxes on both strands.
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  Random DNA/RNA mutatorRandom substitutions, insertions and deletions at a chosen rate.
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  Melting temperature (TM) calculatorTM of DNA/DNA, RNA/RNA and DNA/RNA duplexes.
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  CRISPR/Cas9 guide RNA generatorPAM sites and guide RNAs in your sequence or in 25 bacterial genomes.
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  PCR annealing temperatureAnnealing temperature for Taq, Phusion and Q5, including multiplex PCR.

Extended Bioinformatics Web Services (ExBWS)

Six further tools. Described in Penchovsky, Pavlova and Kaloudas, Int. J. Bioinformatics Research and Applications (2021), funded by BNSF grant KP-06-H31/18/13.12.2019.

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  DNA/RNA translatorTranslation in all six frames with five genetic codes.
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  AminoCODEConvert protein sequences between one- and three-letter codes.
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  Virtual PCRPredicted product and yield from a template and two primers.
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  Hydropathy plotKyte-Doolittle or Moon-Fleming hydropathy of a protein.
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  Reverse translatorProtein to DNA with the preferred codons of 10 hosts.
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  Eukaryotic ORF finderORFs, TATA boxes, intron borders and pyrimidine-rich regions.

Database

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  RSwitch database215 riboswitches of 16 types as antibacterial drug targets.

Ribozyme design software

Programs for Linux/Unix that generate hammerhead allosteric ribozymes, based on algorithms published in Nature Biotechnology. GHOST-YES and GHOST-NOT are described in the Journal of Biotechnology (2023) and released under the GNU GPL v3. They are free for academic research: contact us to get them. Installation guide (PDF).

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  GHOST-YES and GHOST-NOTFast oligonucleotide-sensing allosteric ribozymes with YES or NOT logic.
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  Oligonucleotide-sensing ribozyme generatorAllosteric ribozymes with YES logic (Linux/Unix program).
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  Inverse folding ribozyme generatorInverse-folding design of YES-logic ribozymes (Linux/Unix program).

Small utilities

• CalendarA calendar for any month and year.
• Scientific calculatorA calculator in the browser.
• Your IP addressShows the address your computer uses on the internet.

Other bioinformatics websites

• NCBINational Center for Biotechnology Information.
• BLASTSequence similarity search.
• Primer-BLASTPrimer design with specificity check.
• EMBL-EBIEuropean Bioinformatics Institute.
• UCSC Genome BrowserGenome assemblies and annotation.
• RfamRNA families, including riboswitches.
• RCSB PDBProtein and nucleic acid structures.
• KEGGPathways and genomes.
• BioCycPathway/genome databases.

FMN binding its riboswitch aptamer