/Splinter

Set of simple tools to generate various types of hypothetical mutant DNA/RNA sequences from a single wildtype sequence. Mutagen.py takes as its input a single wildtype sequence and generates all the single_mutation permutations of that sequence. Ideally it reports the quantity of permutations and dumps all the hypothetical sequences to one of several filetypes for analysis.

Primary LanguagePython

Welcome to Splinter (v1.0)

Splinter is a simple command line script intended to be used as a full coverage mutant library generator. It was originally created as a quick and nasty script for generating mutant DNA libraries. I could not find any applications on the internet that do this, so here's mine.

The research in [the lab where Iused to work] (http://yokobayashilab.net), focuses on probing the secondary structure of functional ribozymes, by assaying full coverage single and double replacement mutant libraries of some wildtype sequence of interest. See [Kobori, et al. 2015] (https://www.ncbi.nlm.nih.gov/pubmed/27461281) for an example of this research. This is a similar approach to that used in [Double Mutant Cycle Analysis] (http://www.sciencedirect.com/science/article/pii/S1359027896000569) for protein structure probing.

How Splinter Works

Splinter runs in [Python3] (https://www.python.org/downloads/) from the command line. Just download the file mutagen.py and save it to your working directory. Then run it from the command line as follows:

bioinfo:home$ python /home/path-to-working-directory/mutagen.py

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx WELCOME TO SPLINTER xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

etc...

Follow the command line prompts, and you're bound to come right.

Dependencies

[Numpy1.1] (http://www.numpy.org) or higher.
[pandas0.19] (http://pandas.pydata.org) or higher.

Input

It takes from the user a single wildtype DNA sequence, with bases from non-mutable regions in lowercase and bases from the mutable regions in uppercase:

For example, your input/wildtype sequence is:

acACGTgt

All mutant bases in lowercase will be fixed, whereas the uppercase bases will be mutated. So for example, the input above would generate a single deletion library of four sequences for full coverage of the mutable region:

ID	        Sequence	Mutation
Wildtype	acACGTgt	
0	        AC_CGTGT	A3, 
1	        ACAC_TGT	G5, 
2	        ACA_GTGT	C4, 
3	        ACACG_GT	T6,

And similarly for the double deletion, triple deletion, single replacement and double replacement mutant libraries. All libraries are output to an excel file, which most manufacturers (e.g. [IDT] (http://sg.idtdna.com/site)) will accept to produce your oligonucleotides.

Contact

I have much to learn, so feel free to email me if you have any questions, comments, concerns and/or suggestions about the code.

Crys

larvalanobium(at)gmail.com