AMPK Methods and Protocols
Towler MC, Hardie DG (2007) AMP-activated protein kinase in metabolic control and insulin signaling. Circ Res 100:328–341 Leff ...
Chapter 8 Studying AMPK in an Evolutionary Context Arpit Jain, Valentin Roustan, Wolfram Weckwerth, and Ingo Ebersberger Abstrac ...
To increase the precision of evolutionary conclusions that can be drawn from phylogenetic profiles, it is common to use the subs ...
particular tool over the one that we have listed, it is easy to substi- tute it in the analysis workflow (Fig.1). All analyses c ...
sequences. An FTP server (ftp://ftp.ncbi.nlm.nih.gov/genomes) facilitates the bulk download even of larger selections of genomes ...
2.3.2 OMA [23] OMA (http://omabrowser.org/oma/home/) is a comprehensive database providing access to precomputed orthologs on di ...
[29]. The tool is integrated into the HaMStR package (https:// github.com/BIONF/HaMStR). 2.4.4 DoMosaics [30] DoMosaics (http:// ...
3 Methods 3.1 Collecting the Pathway Components Identify the pathway of interest and download the involved protein sequences in ...
redundancies due to proteins being represented both in Swiss- Prot and TrEMBL. Choose “Download” from the menu and select “Fast ...
Compiling the sequence databases for your study is a critical task, but analysis scenarios are too diverse to give an all-embrac ...
don’t be too sparse in your taxon sampling, as otherwise evo- lutionary conclusions depend too heavily on individual species and ...
Open the URLhttp://www.orthodb.org/. You can query the database for ortholog of your seed protein using (1) the protein sequenc ...
Train a profile hidden Markov model usinghmmbuildfrom the HMMER package [31]:hmmbuild PRKAA1.hmm PRKAA1. aln. Create two direct ...
-refspec¼seedSpecies -coreOrth¼4 -minDist¼genus -max- Dist¼kingdom -strict -checkCoorthologsRef -representative -cleanup. “minDi ...
3.4 Assessing the Feature Architecture Similarity (FAS) Between Proteins This protocol allows analyzing and comparing feature ar ...
reason at this level to assume that the two proteins have diverged in their functionality. Feature Architecture Similarity (FAS) ...
To later visualize the information for all pathway proteins in one go, you need to combine the contents of the files ending in ...
outline the routine for species represented in the QfO reference proteome collection, as the sequences in these sets are availab ...
Run the application and upload the customized phylogenetic profile matrix (AMPK_1.matrix) as input file (seeNote 10). Upload fu ...
Species Proteins PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2 PRKAG3 1001_Chordata1002_Cnidaria 1003_Platyhelminthes 1004_Nematoda1 ...
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