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Main.HomePage History
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February 26, 2019, at 12:54 PM
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Source code is available [[https://www.bioinformatics.org/groups/?group_id=1255 | here]] and is published under the GPL for free use and distribution.
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Source code is available [[https://www.bioinformatics.org/groups/?group_id=1255 | here]] under 'Downloads' and is published under the GPL for free use and distribution.
February 25, 2019, at 10:09 PM
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These tools enable measurement of functional and structural distance between closely related organisms (ex: strains of E.coli) and between domains of life (ex: Prokaryotes and Eukaryotes).
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These tools enable measurement of functional and structural distance between closely related organisms (ex: strains of ''E. coli'') and between domains of life (ex: Prokaryotes and Eukaryotes).
February 25, 2019, at 10:09 PM
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Written by Andrew Kettring of the Sean D. Moore lab at the University of Central Florida.
See the [[https://www.bioinformatics.org/phylometaprot/wiki/Main/AboutThisSite | About]] page for more information! to:
See the [[https://www.bioinformatics.org/phylometaprot/wiki/Main/AboutThisSite | About]] page for more information on installation and usage.
Written by Andrew Kettring of the Sean D. Moore lab at the University of Central Florida. February 25, 2019, at 10:08 PM
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These tools enable measurement of functional and structural distance between both closely related organisms, and between domains of life (ex: Prokaryotes and Eukaryotes).
to:
These tools enable measurement of functional and structural distance between closely related organisms (ex: strains of E.coli) and between domains of life (ex: Prokaryotes and Eukaryotes).
February 25, 2019, at 10:03 PM
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February 25, 2019, at 10:01 PM
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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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See the [[https://www.bioinformatics.org/phylometaprot/wiki/Main/AboutThisSite | About]] page for more information! February 25, 2019, at 09:57 PM
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INPUT
Batches of whole proteomes (.FAA), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
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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INPUT
Batches of whole proteomes (.FAA), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
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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.
February 25, 2019, at 09:54 PM
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Written by Andrew Kettring of the Sean D. Moore lab at the University of Central Florida.
February 25, 2019, at 09:52 PM
by 99.117.188.235 -
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Source code is available [[https://www.bioinformatics.org/groups/?group_id=1255 | here]], and is published under the GPL for free use and distribution.
to:
Source code is available [[https://www.bioinformatics.org/groups/?group_id=1255 | here]] and is published under the GPL for free use and distribution.
February 25, 2019, at 09:51 PM
by 99.117.188.235 -
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PhyloMetaProt supports parallel processing for BLAST-based operations, which are notably processor intensive.
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Parallel processing is supported for BLAST-based operations and is highly recommended.
February 25, 2019, at 09:50 PM
by 99.117.188.235 -
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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 requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip to obtain packages.
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Example input data is included for all three modules.
February 25, 2019, at 09:49 PM
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Source code is available [[https://www.bioinformatics.org/groups/?group_id=1255 | here]], and is published under the GPL for free use and distribution.
February 25, 2019, at 09:41 PM
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-Requirements-
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython
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REQUIREMENTS
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip to obtain packages
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-Where to get input data-
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February 25, 2019, at 09:37 PM
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Welcome to the Phylogenomics by Metabolomics and Proteomics Tools (aka: PhyloMetaProt) homepage!
These tools enable measurement of functional and structural distance between both closely related organisms, and between domains of life (ex: Prokaryotes and Eukaryotes).
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)
INPUT
Batches of whole proteomes (.FAA), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
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.
UNDER THE HOOD
PhyloMetaProt is written for Python 2.7 and uses a command line interface.
PhyloMetaProt supports parallel processing for BLAST-based operations, which are notably processor intensive.
-Requirements-
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython
The pairwise_prot_blast module also requires installation of NCBI's BLAST executables.
-Where to get input data-
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.
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