Warning

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

Glue

Library diversity and completeness (Acronymn means?)

Description

Given a library of L sequences, where each sequence is chosen at random from a set of V equiprobable variants, we wish to calculate the expected number of distinct (i.e. unique) sequences represented in the library. Alternatively, given a set of V equiprobable variants, we wish to calculate the library size L necessary to obtain a given percentage completeness, or to have a given probability of being 100% complete. (Typically assuming V >> 1, e.g. V > 10.)

Example ( show)

For the default values on the web server, there are a total of one million possible variants. This is roughly equivalent to an oligonucleotide directed randomization experiment involving four NNS codons (which gives V = 324 = 1048576).

In the first panel, the experimenter has constructed a library of three million transformants and wishes to estimate how many of the one million possible variants are represented in the library. The answer is ~95.02% or 950200 variants.

In the second panel, s/he knows that there are one million possible variants, and wants to know how big her/his library should be in order to ensure that ~95% of them (i.e. 950000 variants) are represented. The answer is that a library of ~2.996 million transformants is required.

In the ideal situation her/his library would contain all one million variants. In the third panel s/he calculates the library size required in order to be 95% sure of complete representation. The answer is ~16.79 million transformants.

Calculations

N variants

Library size

Completeness

prob 100% complete


Glue-IT —amino acid level

GlueIT

Description

Programme to find the expected amino acid completeness of a given library (not counting any variants with introduced stop codons) where the sequences in the library are chosen at random from a set of XYZ codon variants (where X,Y,Z are standard nucleotide codes chosen by the user, e.g. XYZ = NNS [N = A/C/G/T; S = C/G; 32 possible equiprobable codon variants; 20 + 1 possible non-equiprobable amino acid/stop codon variants]). Up to six codons may be independently varied.

To calculate the library size required in order to obtain a given completeness, or to have a given probability of being 100% complete, just try entering different library sizes and check the resulting library statistics until you home in on your required values.

I'll need to make options for glue1AA

Input

Library size

Varied codons
Scheme

Scheme

Scheme

Scheme

Scheme

Scheme