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tutorials:eccb_t2_fundi [2012/09/06 17:33] romainstuder created |
tutorials:eccb_t2_fundi [2012/09/06 22:10] (current) romainstuder |
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| - | ### FunDi | + | ==== FunDi ==== |
| - | Installation: | + | === Installation === |
| Download it from https://github.com/dgaston/FunDi | Download it from https://github.com/dgaston/FunDi | ||
| - | => ZIP buttom | + | => ZIP button |
| + | Install it with these commands: | ||
| <code> | <code> | ||
| unzip dgaston-FunDi-229c4d6.zip | unzip dgaston-FunDi-229c4d6.zip | ||
| Line 28: | Line 29: | ||
| FunDi needs PERL release 5.10 or higher (maybe with threads enabled). | FunDi needs PERL release 5.10 or higher (maybe with threads enabled). | ||
| - | Execution: | + | |
| + | |||
| + | |||
| + | |||
| + | ==== Identication of function sites in the Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (EC 1.2.1.12) enzyme ==== | ||
| + | |||
| + | === Execution === | ||
| <code> | <code> | ||
| perl FunDi.pl -a GAPDH_alignment.phy -o gapdh_subtree -m LG -s gapdh_subtree.def -P qmmraxml -r 4 -t gapdh.tre | perl FunDi.pl -a GAPDH_alignment.phy -o gapdh_subtree -m LG -s gapdh_subtree.def -P qmmraxml -r 4 -t gapdh.tre | ||
| </code> | </code> | ||
| + | (It can take time) | ||
| - | => Results are in file FunDi_Posterior_Scores.txt | + | Parameters: |
| + | * -a: multiple alignment file in PHYLIP format. | ||
| + | * -o: basename for output. | ||
| + | * -m: Substitution matrix (qmmraxml => LG). | ||
| + | * -s: definition of groups, one line = one subgroup. | ||
| + | * -P: phylogenetic tool to estimate parameters. | ||
| + | * -r: number of categories for the gamma distribution. | ||
| + | * -t: phylogenetic tree in NEWiCK format. | ||
| - | You can load it in your spreadsheet (tab separated, activate special detection of numbers). | + | More details with the help: |
| - | The numbering of sites starts from 0. | + | <code> |
| - | Sites with a posterior probality P(FD) with 0.50 or more could be interesting. | + | perl FunDi.pl -h |
| + | </code> | ||
| + | |||
| + | === Results === | ||
| + | |||
| + | == Visualisation of sites == | ||
| + | |||
| + | The most important file is "FunDi_Posterior_Scores.txt".\\ | ||
| + | You can load it in your spreadsheet (tab separated, activate special detection of numbers).\\ | ||
| + | The numbering of sites starts from 0.\\ | ||
| + | Sites with a posterior probality P(FD) with 0.50 or more could be interesting.\\ | ||
| + | In particular:\\ | ||
| + | * site 38 (= 39 in Jalview) (= 34 in the structure 2PKQ) | ||
| + | * site 193 (=194 in Jalview) (=188 in the structure 2PKQ) | ||
| + | * site 195 (=196 in Jalview) (=191 in the structure 2PKQ) | ||
| + | |||
| + | Open Jalview, load the file GAPDH_alignment.phy, remove the first line and visualisation the sites. | ||
| + | |||
| + | |||
| + | == 3D visualisation == | ||
| + | |||
| + | Open PyMol and load protein 2PKQ | ||
| + | <code> | ||
| + | Plugins-> PDB Loader Service | ||
| + | </code> | ||
| + | |||
| + | Change the visualisation mode | ||
| + | <code> | ||
| + | all->S->Show->as->Cartoon | ||
| + | all->C->Color by->chain | ||
| + | </code> | ||
| + | |||
| + | In the PyMol command line, select the sites of interest... | ||
| + | <code> | ||
| + | select ImportantSites, resi 34+188+191 | ||
| + | </code> | ||
| + | ... and change the visualisation mode: | ||
| + | <code> | ||
| + | (ImportantSites)->S->Show->Spheres | ||
| + | (ImportantSites)->C->Color by->chain | ||
| + | </code> | ||
