publication . Article . 2012

Pythoscape: a framework for generation of large protein similarity networks

Babbitt, Patricia; Barber, AE; Babbitt, PC;
  • Published: 01 Sep 2012
  • Publisher: Oxford University Press (OUP)
  • Country: Mexico
Abstract
Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network nodes or edges enables hypothesis creation about sequence–structure–function relationships across sets of related proteins. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines se...
Subjects
free text keywords: Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications, Bioinformatics, Software, business.industry, business, Protein similarity, Theoretical computer science, Data mining, computer.software_genre, computer, Node (networking), Visualization, Data display, Data collection, Pairwise comparison, Computer science, Python (programming language), computer.programming_language, Applications Note, Sequence Analysis
Related Organizations
Funded by
NIH| Laying the Foundation of Genomic Enzymology
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2R01GM060595-14
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| PHARMACEUTICAL SCIENCES AND PHAMOCOGENOMICS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5T32GM007175-35
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

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