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Codon choice

Description

This helper allows you to pick the most ideal degenerate codons. It comes in two forms. You choose the required amino acids or you choose the codons to inspect.

By codon ( show)



Scheme

By amino acids ( show)

This section would be cool if it had a negative option and stuff like, hydrophobics use Z.

It sorts with a 2x penalty for stop and give precence to more equal distributions, in case of a tie to less degenerate codons.

Accepts three letter code with first letter capital separated by a space, or one letter with spaces or not — corner case: SER is Ser + Asp + Arg while Ser is Serine.

Wanted AAs
Please choose at least one amino acid
Unwanted AAs

About

Authors

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Background


This is a revamp and serious expansion of the old server by Wayne Patrick and Andrew Firth found Here.

Links

FAQ

Feeling lexicologically challenged or have a common question?

MF's Github: Mutagenesis

The mutagenesis module to handle point mutants

MF's Github: Pedel2

What to run this server locally or copy paste something?

Navigation

Feedback
Various links Citation Github








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Citations

This site contains several tools with different citations.

  • Various tools to be published
  • Deepscan and Mutant primers Acevedo-Rocha CG, Ferla M, Reetz MT. Directed Evolution of Proteins Based on Mutational Scanning. Methods Mol Biol. 2018;1685:87-128. doi:10.1007/978-1-4939-7366-8_6
  • Quick quality control Acevedo-Rocha CG, Reetz MT, Nov Y. Economical analysis of saturation mutagenesis experiments. Sci Rep. 2015;5:10654. Published 2015 Jul 20. doi:10.1038/srep10654
  • Mutanalyst Ferla MP. Mutanalyst, an online tool for assessing the mutational spectrum of epPCR libraries with poor sampling. BMC Bioinformatics. 2016;17:152. Published 2016 Apr 4. doi:10.1186/s12859-016-0996-7
  • Pedel Patrick WM, Firth AE, Blackburn JM. User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Eng. 2003;16(6):451-457. doi:10.1093/protein/gzg057
  • PedelAA and Glue-it Firth AE, Patrick WM. GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries. Nucleic Acids Res. 2008;36(Web Server issue):W281-W285. doi:10.1093/nar/gkn226

Overview

Links to academic resources and academic social media presence of the authors

Matteo Ferla's Blog Carlos Acevedo-Rocha's Twitter Matteo Ferla's homepage Michelanglo (create, edit and share interactive protein views) Matteo Ferla's Twitter (inactive)