Warning

Matteo just upgraded both Bootstrap and Font Awesome, and did a major change to the Mako templating so bugginess is a given.

Aim

Engineering better proteins is a multifaceted task. Here you will find an assortment of tools that will help you find a better variant at every step of the way.

There are many technical terms in protein design and engineering, so if you are struggling with terminology do check out the glossary and FAQ page.

Applications

Primers — Mutant primers:
Given a sequence and list of desired mutations it will return primers to make each of those mutations.
Primers — Deepscan:
Given a sequence and a codon, say GCT for alanine scanning, it will return a list of all primers needed to scan the sequence with that mutation
epPCR — Mutantcaller:
Given a sequence and an ab1 trace it will return all mutations present and also list heterozygous sites (say you have a mixed population or you pooled two or three variants to cut down on sequencing)
epPCR — Mutantanalyst:
Given a sequence and a list of sampled variants, it will say how biased the library is.
epPCR — Pedel:
Given a sequence, mutational spectrum and mutational load, it will say how redundant is the library.
epPCR — PedelAA:
Given a sequence, mutational spectrum and mutational load, it will say how redundant is the library from an amino acid point of view.
epPCR — Chances:
Given a sequence and a desired mutation, it will say what are the chances that mutation ought to have been seen.
epPCR — Generator:
Given a sequence and mutational bias data, it generate mutations.
Glue — Glue:
Calculates how complete a library is from a coupon collectors problem standpoint.
Glue — GlueIT:
Calculates the completeness of a library mutated at 1–6 codons.
Driver:
Calculates the probability of cross-over events
QQC (Quick quality control) calculator:
Given an ab1 file of a sequence pool mutated at a codon, it gives the distribution of nucleotides and codons.
Landscape:
Given a series of Rosetta pmut_scan outputs it shows the mutational landscape of that protein
Codon helper
A tool to help you pick the best degenerate codons. Also found in any page that requires codons as a sequence.

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