kmdalton / scaled Goto Github PK

Develop function to generate clustal alignment file given an amino acid sequence, or a PDB flie and chain ID. Dependent on availability of practical BLASTP and EMBL-EBI APIs.

Allow pysca code to be portable by removing hard-coded DLL dependencies and developing easy installation and tutorial instructions for all major operating systems.

To make this version more portable, we need to go through the code and make sure dependency locations are not hard coded.

In general, for now, should we assume all files are located in the same folder?

If this project expands, I could imagine making categories of files ('core','analysis','graphing') etc.

This isn't an issue if we use a web GUI, but currently the EMBOSS package which includes the Waterman alignment does not exist for windows (also seems like it will be deprecated)

Since we're doing the web GUI, and hopefully automating all steps, then I propose we implement the change that the first sequence in the sequence alignment matrix is the sequence of interest (i.e. the submitted PDB file).

title says it all.

Generate web-interface for pysca, through CGI-scripting. The web interface should accept a residue sequence or a clustal alignment file, allow the user to choose between some options, and download "results".

Results should be a residue coevolution matrix, a sequence covariance matrix, and an ipynb file which walks users through the analysis of the data. If a PDB file is supplied, then a PDB file is returned with each cluster identified by a unique chain number.