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Main.AboutThisSite History
Hide minor edits - Show changes to output
February 26, 2019, at 01:42 PM
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Batches of whole proteomes (.FAA), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
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Batches of whole proteomes (.faa), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
February 26, 2019, at 01:42 PM
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Distance matrices and pairwise lists of distances between each of the supplied proteomes/metabolomes in the batch. Competition and complementarity matrices are generated for seed/non-seed analyses.
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All output files will propagate in the ./outfiles/ subdirectory.
For the pairwise_prot_blast and pairwise_paths modules, output includes distance matrices and pairwise lists of distances between each of the supplied proteomes/metabolomes in the batch. Competition and complementarity matrices are generated for seed/non-seed analyses.
February 26, 2019, at 01:40 PM
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Run the analyses using python2 <module_name>.py
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Run the analyses using
> python2 <module_name>.py
February 26, 2019, at 01:39 PM
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Proteomes can be downloaded using NCBI's [[https://www.ncbi.nlm.nih.gov/Traces/wgs/?view=wgs | WGS browser]] or can supplied by the user.
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Proteomes can be downloaded using NCBI's [[https://www.ncbi.nlm.nih.gov/Traces/wgs/?view=wgs | WGS Browser]] or can supplied by the user.
February 26, 2019, at 01:37 PM
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No installation is required to use the PhyloMetaProt modules.
Unzip the package into a desirable directory.
Place the files intended to be analyzed in the module's ./infiles/ subdirectory.
Using a command shell, navigate to the module's directory.
Run the analyses using python2 <module_name>.py
February 26, 2019, at 01:32 PM
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'''ABOUT'''
PhyloMetaProt is written for Python 2.7 and uses a command line interface.
Parallel processing is supported for BLAST-based operations and is highly recommended.
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PhyloMetaProt is written for Python 2.7 and uses a command line interface.
Parallel processing is supported for BLAST-based operations and is highly recommended.
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip2 to obtain packages. Users should check to ensure the packages are installed for Python 2.7, rather than Python 3.X
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PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip2 to obtain packages. Users should check to ensure the packages are installed for Python 2.7, rather than Python 3.X.
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Proteomes can be downloaded using NCBI's WGS browser or can supplied by the user.
The pairwise_paths module was intended for use with PathwayTools, but should also function with KEGG. Any exported list of metabolic pathways should work for input!
The pairwise_seeds module requires that SBML formatted reaction networks be pre-processed by NetSeed.
to:
Proteomes can be downloaded using NCBI's [[https://www.ncbi.nlm.nih.gov/Traces/wgs/?view=wgs | WGS browser]] or can supplied by the user.
The pairwise_paths module was intended for use with [[http://bioinformatics.ai.sri.com/ptools/| PathwayTools]], but should also function with KEGG. Any exported list of metabolic pathways should work for input!
The pairwise_seeds module requires that SBML formatted reaction networks be pre-processed by [[http://borensteinlab.com/software_netseed.html | NetSeed]].
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'''USAGE'''
For each module
February 26, 2019, at 01:10 PM
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PhyloMetaProt is written for Python 2.7 and uses a command line interface.
Parallel processing is supported for BLAST-based operations and is highly recommended.
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PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip to obtain packages.
to:
PhyloMetaProt is written for Python 2.7 and uses a command line interface.
Parallel processing is supported for BLAST-based operations and is highly recommended.
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip2 to obtain packages. Users should check to ensure the packages are installed for Python 2.7, rather than Python 3.X
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February 26, 2019, at 11:56 AM
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The pairwise_seed module requires that SBML formatted reaction networks be pre-processed by NetSeed.
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The pairwise_seeds module requires that SBML formatted reaction networks be pre-processed by NetSeed.
February 26, 2019, at 11:56 AM
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February 25, 2019, at 10:06 PM
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Proteomes can be downloaded using NCBI's WGS browser, or can supplied by the user.
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Proteomes can be downloaded using NCBI's WGS browser or can supplied by the user.
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For clustering and visualization of phylograms, we recommed the use of MEGA from NCBI.
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For clustering and visualization of phylograms we recommend the use of MEGA from NCBI.
February 25, 2019, at 10:02 PM
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PhyloMetaProt is written for Python 2.7 and uses a command line interface.
Parallel processing is supported for BLAST-based operations and is highly recommended.
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UNDER THE HOOD
PhyloMetaProt is written for Python 2.7 and uses a command line interface.
Parallel processing is supported for BLAST-based operations and is highly recommended.
to:
February 25, 2019, at 09:59 PM
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This is a default page.(:if ! auth edit:)
[[{$Name}?action=login | $[Login] ]](:ifend:) to:
MODULES
pairwise_prot_blast - Comprehensive BLASTp distance analysis between whole proteomes
pairwise_paths - Distance analysis from metabolic pathways
pairwise_seeds - Competition and complementarity of metabolic dependencies (seeds)
UNDER THE HOOD
PhyloMetaProt is written for Python 2.7 and uses a command line interface.
Parallel processing is supported for BLAST-based operations and is highly recommended.
REQUIREMENTS
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip to obtain packages.
The pairwise_prot_blast module also requires installation of NCBI's BLAST executables.
INPUT
Batches of whole proteomes (.FAA), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
Proteomes can be downloaded using NCBI's WGS browser, or can supplied by the user.
The pairwise_paths module was intended for use with PathwayTools, but should also function with KEGG. Any exported list of metabolic pathways should work for input!
The pairwise_seed module requires that SBML formatted reaction networks be pre-processed by NetSeed.
Example input data is included for all three modules.
OUTPUT
Distance matrices and pairwise lists of distances between each of the supplied proteomes/metabolomes in the batch. Competition and complementarity matrices are generated for seed/non-seed analyses.
For clustering and visualization of phylograms, we recommed the use of MEGA from NCBI.
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