CATH - tutorials

eccb_t2_badasp

Anonymous (anonymous@undisclosed.example.com) — 2012-09-08T16:15:28+00:00

BADASP BADASP can produce different measures: * bad: similar the Type II of functional divergence. The threshold to choose depend if we want to be stringeant (i.e. BAD > 4) or more relaxed (BAD > 2). * badn = BADN variant of BAD: similar the Type I

eccb_t2_codeml

Anonymous (anonymous@undisclosed.example.com) — 2012-09-09T09:47:06+00:00

CodeML/PAML Install of PAML Download it from here: Windows (The bin/ folder already contains windows executables): cd paml4.6/ Linux: cd paml4.5/ rm bin/*.exe cd src make -f Makefile ls -l rm *.o mv baseml basemlg codeml pamp evolver yn00 chi2 ../bin chmod +x ../bin/*

eccb_t2_diverge

Anonymous (anonymous@undisclosed.example.com) — 2012-09-07T16:47:34+00:00

Diverge2 There is a self-extracting archive at this website: We want to analyse the GAPDH family. Dowload the following files (alignment and 3D structure), unzip them and load them into Diverge2: * * In the “Clustering” tab, select “

eccb_t2_fundi

Anonymous (anonymous@undisclosed.example.com) — 2012-09-06T21:10:43+00:00

FunDi Installation Download it from => ZIP button Install it with these commands: unzip dgaston-FunDi-229c4d6.zip cd dgaston-FunDi-229c4d6/ unzip qmmraxml.zip export PATH=$PATH:qmmraxml # Or mv qmmraxml/qmmraxmlHPC to a PATH folder if not working, you may need to recompile qmmraxmlHPC

eccb_t2_studer

Anonymous (anonymous@undisclosed.example.com) — 2012-09-09T10:31:08+00:00

Practical Introduction The presentation is available here: Useful tools Jalview: (It could be better to increase the memory allocated to java: ) PyMOL: (or ) NJplot: Part I on amino acids dataset: * BADASP: Analysis of the V-type proton ATPase 116 kDa subunit…

eccb_t2_tdg09

Anonymous (anonymous@undisclosed.example.com) — 2012-09-08T16:26:13+00:00

TDG09 Installation Download from here: => tdg09.zip unzip tdg09.zip Detection of site in the Influenza Virus Hemagglutinin HA1 chain We would like to know which sites are important between the Hemagglutinin HA1 of the virus in Avian (genes starting with Av_) and in Human (genes starting with Hu_).

impact_oct_09

Anonymous (anonymous@undisclosed.example.com) — 2015-09-17T10:48:50+00:00

An Introduction to CATH And Gene3D Welcome to the CATH-Gene3D suite of resources for structural annotation, comparison and prediction. ---------- Tutorial Map * * * * * * * * * * * * ---------- ---------- A Brief Introduction

index

Anonymous (anonymous@undisclosed.example.com) — 2023-09-28T16:20:14+00:00

Tutorials CATH-AlphaFlow ISMB/ECCB 2023 Tutorial CATH-AlphaFlow is a Nextflow pipeline developed by CATH and the UCL Advanced Research Computing Centre. The pipeline runs various modules of a new version of CATH-Assign, called CATH-AF-CLI. Each module can be ran individually, or as batches via NextFlow.

mali_nov_09

Anonymous (anonymous@undisclosed.example.com) — 2015-09-21T14:29:47+00:00

An Introduction to CATH And Gene3D Welcome to the CATH-Gene3D suite of resources for structural annotation, comparison and prediction. ---------- Tutorial Map * * * * * * * * ---------- ---------- A Brief Introduction At the heart of the system is the CATH classification of protein domains, derived from integrated semi-automatic processing and manual-curation of high-resolution 3D structures in the wwPDB. From these structures protein domains are identified and co…

mali_tutorial

Anonymous (anonymous@undisclosed.example.com) — 2015-09-22T14:07:59+00:00

Tutorial on CATH and Gene3D