Selected article for: "jmol protein and protein structure"
Author: Pickett, Brett E.; Sadat, Eva L.; Zhang, Yun; Noronha, Jyothi M.; Squires, R. Burke; Hunt, Victoria; Liu, Mengya; Kumar, Sanjeev; Zaremba, Sam; Gu, Zhiping; Zhou, Liwei; Larson, Christopher N.; Dietrich, Jonathan; Klem, Edward B.; Scheuermann, Richard H.
Title: ViPR: an open bioinformatics database and analysis resource for virology research
  • Document date: 2011_10_17
    • ID: 48ym7eti_15
    Snippet: The data in ViPR can be analyzed using a suite of comparative genomics analysis and visualization tools including phylogenetic tree reconstruction with the FastME, RAxML or PhyML algorithms (18) (19) (20) , tree manipulation with Archaeopteryx (21) and evolutionary model optimization with modelTest (22); multiple sequence alignments calculated with MUSCLE (23) and visualized with JalView (24,25), 3D protein structure and sequence feature visualiz.....
    Document: The data in ViPR can be analyzed using a suite of comparative genomics analysis and visualization tools including phylogenetic tree reconstruction with the FastME, RAxML or PhyML algorithms (18) (19) (20) , tree manipulation with Archaeopteryx (21) and evolutionary model optimization with modelTest (22); multiple sequence alignments calculated with MUSCLE (23) and visualized with JalView (24,25), 3D protein structure and sequence feature visualization with Jmol (26), a metadatadriven comparative genomics automated workflow, BLAST (27) , sequence variation analysis using sequence logos (28), a protein sequence pattern matching tool and the automated Genome Annotation Transfer Utility (29) . Several of these tools will be described in more detail within the context of the comparative analysis use case described below.

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