phosp_hotspots's Introduction
# phosp_hotspots scripts 00.* produce output files that can be plotted using 01.plot_outfile.py running the scripts requires previous alignment of protein domains sequences - I cut out the domains out of proteins and put the number of the start of the domain in fasta header. It is possible to use full protein alignment, but I have no idea how well that works. Depending on alignment, two 00. scripts are available. If the pdb is known, 00.phosp_hotspots.py should be used, with the variable pdb_name+domain_start updated in script as in pdb_name;start in alignment. if you do not want to map PDB, you can use the 00.full_alignment.py script, it requires the same files. # required knowledge: alignment with domains cut out out of proteins what pdb to map to (its sequence has to be in alignment)- its name and start of the domain where are the phosphorylations if theres regs/ active sites # required files: alignment.ali all_phosps regulatory -------these two can be empty, but have to exist active_sites------these two can be empty, but have to exist # how to prepare alignment.ali (example for PF00022 uploaded) its an alignment in ONE LINE fasta format, (https://www.biostars.org/p/9262/) with headers like >id; int domain_start; int domain_end domain_start is necessary for correct phosphorylations assignment eg >FBpp0270092 pep:known chromosome:GCA_00 ;196;492 --------Y-EILEV----------------------------IGKG------ >NONE_15409 , MEDTR2G085200.1 ;134;418 --------F-EKLDK----------------------------IGQG------ # how to prepare all_phosps phospho file has to contain the protein id and the position, however script is set up to recognise pfam_scan.pl output which looks like this: SPECIES/ANIMALS/Celegans.phosp_output:Celegans, B0218.3, 191, T, PF00069.24, 35, 319, Pkinase SPECIES/ANIMALS/Celegans.phosp_output:Celegans, B0218.3, 193, Y, PF00069.24, 35, 319, Pkinase SPECIES/ANIMALS/Celegans.phosp_output:Celegans, B0545.1a, 533, S, PF00069.24, 375, 628, Pkinase SPECIES/ANIMALS/Celegans.phosp_output:Celegans, B0545.1a, 534, T, PF00069.24, 375, 628, Pkinase SPECIES/ANIMALS/Celegans.phosp_output:Celegans, B0545.1a, 538, T, PF00069.24, 375, 628, Pkinase If this is not the case, correct line annotations are required in "phos_dataframe" fucntion # how to prepare regulatory these are confirmed human regulatory sites obtained from phosphosite plus database S, 742, P33981, T, 312, P80192, T, 170, O00444, Y, 221, Q13164, T, 260, Q8IWQ3, T, 472, O00311, is enough # how to prepare active its the output of pfam_scan.pl, with the list of prediceted active sites at the end of line so: A2ZVI7_8293 66 324 66 324 PF00069.24 Pkinase Domain 1 264 264 245.8 4.3e-73 1 CL0016 predicted_active_site 211,189 A3A2W5_8676 13 304 13 304 PF00069.24 Pkinase Domain 1 264 264 227.6 1.6e-67 1 CL0016 predicted_active_site 157,138 A3A2W5_8678 13 304 13 304 PF00069.24 Pkinase Domain 1 264 264 227.6 1.6e-67 1 CL0016 predicted_active_site 157,138 if the active sites are any different the "active_dataframe" requires updating # what variables to edit in 00.run_phosps_hotspots.py: 240 how_many_permuts=100####################HOW MANY PERMUTS (100 is the usual, but can be more or less) treshold and fore_val - pvalue threshold and foreground value that will allow hotspot (only in 00.phosp_hotspots.py) # usage run 00. script in the same folder as the alignment.ali, all_phosp, regulatory and active_sites. The output will be, depending on version of 00. either pval_pdb or pval_full_ali. Change input in 01. to plot.
phosp_hotspots's People
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. ๐๐๐
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.