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Pythoscape specifications


Unique identifier OMICS_13181
Name Pythoscape
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.04
Stability Stable
Maintained Yes


No version available



  • person_outline Patricia Babbitt <>

Publication for Pythoscape

Pythoscape citations


Prediction of enzymatic pathways by integrative pathway mapping

PMCID: 5788505
PMID: 29377793
DOI: 10.7554/eLife.31097.026

[…] are given as input, as well as the linearity and length of the pathway., a sequence similarity network (ssn) and genome neighborhood network (gnn) were constructed using the efi-est webserver () and pythoscape v1.0 software () for an anchor protein, trap sbps (uniprot id p71336 and uniprot id a7jqx0), to provide candidate pathway members (; ). the network stringency for computing iso-functional […]


A global view of structure–function relationships in the tautomerase superfamily

PMCID: 5818174
PMID: 29184004
DOI: 10.1074/jbc.M117.815340

[…] removal of redundant sequences produced a final, nonredundant set of 11,395 sequences for further analyses., sequence similarity networks were constructed for the tsf using algorithms taken from pythoscape software () and tailored for use with the sfld and its hardware environment. sequences to be considered for each network were compared pairwise in an all-by-all manner using the blast […]


Evaluating Functional Annotations of Enzymes Using the Gene Ontology

PMCID: 5837055
PMID: 27812939
DOI: 10.1007/978-1-4939-3743-1_9

[…] for truly large data sets, they can be easily created and visualised for several thousand sequences. there are many ways to create such networks, the networks created by the sfld are generated by pythoscape [], a freely available software that can be downloaded, installed and can be run locally. recently, web servers have been described that will generate networks for users. for example, […]


Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

PMCID: 4113996
PMID: 24980702
DOI: 10.7554/eLife.03275.025

[…] as regulon analyses and pathway docking to facilitate the discovery of novel enzymes and the metabolic pathways in which they function., the ssns for the prs () and the ocds () were created using pythoscape v1.0 () that is available for download from the input sequences were downloaded from the interpro webpages of prs and ocds: […]


Exploring the Biological and Chemical Complexity of the Ligases

PMCID: 4018984
PMID: 24657765
DOI: 10.1016/j.jmb.2014.03.008

[…] taking all the sequences in the manually annotated portion of uniprotkb (swiss-prot) that are annotated as being a ligase (21,953 sequences from the enzyme.dat file as of august 2012), we used the pythoscape framework to generate the initial representative network. firstly, the all-against-all blast scores are calculated for the initial protein set. then, the protein sequences are clustered […]


Mechanistic and Bioinformatic Investigation of a Conserved Active Site Helix in α Isopropylmalate Synthase from Mycobacterium tuberculosis, a Member of the DRE TIM Metallolyase Superfamily

PMCID: 4025573
PMID: 24720347
DOI: 10.1021/bi500246z

[…] as a query against uniref100 again (73764 hits) and filtered in the same manner to produce the final superfamily set (8817 unique sequences)., sequence similarity networks were generated using the pythoscape program. briefly, the final superfamily set of proteins (8817 unique sequences) were imported into a mysql database and defined as nodes. all-by-all blast2seq runs were performed to define […]

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Pythoscape institution(s)
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
Pythoscape funding source(s)
Supported by Pharmaceutical Research and Manufacturers of America, Achievement Rewards for College Scientists Foundation, NIH Training Grant T32 GM007175 and R01 GM60595.

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