Literature DB >> 12169529

The POPPs: clustering and searching using peptide probability profiles.

Michael J Wise1.   

Abstract

The POPPs is a suite of inter-related software tools which allow the user to discover what is statistically 'unusual' in the composition of an unknown protein, or to automatically cluster proteins into families based on peptide composition. Finally, the user can search for related proteins based on peptide composition. Statistically based peptide composition provides a view of proteins that is, to some extent, orthogonal to that provided by sequence. In a test study, the POPP suite is able to regroup into their families sets of approximately 100 randomised Pfam protein domains. The POPPs suite is used to explore the diverse set of late embryogenesis abundant (LEA) proteins.

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Year:  2002        PMID： 12169529     DOI： 10.1093/bioinformatics/18.suppl_1.s38

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  8 in total

Review 1.  The enigmatic LEA proteins and other hydrophilins.

Authors:  Marina Battaglia; Yadira Olvera-Carrillo; Alejandro Garciarrubio; Francisco Campos; Alejandra A Covarrubias
Journal:  Plant Physiol       Date:  2008-09       Impact factor: 8.340

2.  Gene cloning and characterization of a soybean (Glycine max L.) LEA protein, GmPM16.

Authors:  Ming-der Shih; Shu-Chin Lin; Jaw-Shu Hsieh; Chi-Hua Tsou; Teh-Yuan Chow; Tsai-Piao Lin; Yue-Ie C Hsing
Journal:  Plant Mol Biol       Date:  2005-03-24       Impact factor: 4.076

3.  Role of pro-oncogenic protein disulfide isomerase (PDI) family member anterior gradient 2 (AGR2) in the control of endoplasmic reticulum homeostasis.

Authors:  Arisa Higa; Audrey Mulot; Frédéric Delom; Marion Bouchecareilh; Duc Thang Nguyên; Daniel Boismenu; Michael J Wise; Eric Chevet
Journal:  J Biol Chem       Date:  2011-10-24       Impact factor: 5.157

4.  Functional analysis of the group 4 late embryogenesis abundant proteins reveals their relevance in the adaptive response during water deficit in Arabidopsis.

Authors:  Yadira Olvera-Carrillo; Francisco Campos; José Luis Reyes; Alejandro Garciarrubio; Alejandra A Covarrubias
Journal:  Plant Physiol       Date:  2010-07-28       Impact factor: 8.340

5.  Expression profiling and cross-species RNA interference (RNAi) of desiccation-induced transcripts in the anhydrobiotic nematode Aphelenchus avenae.

Authors:  Wesley Reardon; Sohini Chakrabortee; Tiago Campos Pereira; Trevor Tyson; Matthew C Banton; Katharine M Dolan; Bridget A Culleton; Michael J Wise; Ann M Burnell; Alan Tunnacliffe
Journal:  BMC Mol Biol       Date:  2010-01-19       Impact factor: 2.946

6.  Characterization of two soybean (Glycine max L.) LEA IV proteins by circular dichroism and Fourier transform infrared spectrometry.

Authors:  Ming-der Shih; Tzung-Yang Hsieh; Tsai-Piao Lin; Yue-Ie C Hsing; Folkert A Hoekstra
Journal:  Plant Cell Physiol       Date:  2010-01-12       Impact factor: 4.927

7.  LEAping to conclusions: a computational reanalysis of late embryogenesis abundant proteins and their possible roles.

Authors:  Michael J Wise
Journal:  BMC Bioinformatics       Date:  2003-10-29       Impact factor: 3.169

8.  Molecular analysis of the cold tolerant Antarctic nematode, Panagrolaimus davidi.

Authors:  Michael A S Thorne; Hiroshi Kagoshima; Melody S Clark; Craig J Marshall; David A Wharton
Journal:  PLoS One       Date:  2014-08-06       Impact factor: 3.240
  8 in total

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