ampk-tor.md

AMPK-TOR Demo Data for PhyloProfile Tool

Description

This folder contains phylogenetic profile data for AMPK-TOR pathway, which is based on the work of Roustan et. al (2016). Two additional layers of information integrated to this data is the forward and backward protein domain architecture similarity.

Domain architecture similarity scores are used to compare the protein architecture between seed and its ortholog (Koestler et al. (2010), BMC Bioinformatics). Forward scores indicate the comparison where the domain architectures of seed proteins are used as reference (i.e. missing domains in seed proteins will be penalized). While backward scores are obtained when orthologous proteins are used as reference (i.e. missing domains in orthologs will be penalized).

Content

• Main input file (phylogenetic profile integrated with forward and backward domain similarity scores): ampk-tor.phyloprofile

• Optional Domain files: domains_F ( for forward scores) domains_B (for backward scores) . You can optionally give one of those files under the Additional annotation input upload on the Input & settings page after startup.

• Optional FASTA sequence file: ampk-tor.extended.fa. You can input this file into FASTA config -> Choose location for: Concatenated fasta file.

Different input formats are described in our Input-Data Wiki Page.