 CDTree: a protein domain hierarchy viewer and editor |
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Download CDTree for the PC
(This PC-only download also installs a preview release
of Cn3D 4.2; earlier versions of Cn3D do not work with CDTree.)
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| CDTree is ... |
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a powerful tool to aid in the classification of protein sequences and investigate their evolutionary relationships;
- a web-based helper application used by the CDD on-line search service
to permit user interaction with pre-defined protein domain hierarchies;
- an integrated software environment organized to help users
assimilate large amounts of biological data from various resources by access to a
suite of analysis methods.
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CDTree features include ...
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PSI-BLAST interface for recruiting new
sequences into an existing model
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Use BLAST to seed a domain model from a single
sequence
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Phylogenetic tree analysis
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Taxonomy interface
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Domain architecture interface
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Cross-hit analysis between multiple protein
domain models
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Cn3D 4.2
(preview release) for multiple alignment editing and 3D
structure visualization
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Eliminate redundancy in a domain model, for
example, based on sequence similarity and/or taxonomic representation
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Build a hierarchy of related protein domains whose multiple
alignments are 'self-consistent' (i.e., reflect the common evolutionary relationship modeled by the domain hierarchy)
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Selection mechanism allows for identification of sequences across multiple viewers
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In-Program Help documentation (coming soon: on-line tutorials)
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The screenshot above results from launching CDTree with the
'Interactive Display' buttons on the CDD page for the RNR_PFL domain hierarchy.
Ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL) are structurally similar and are thought to have diverged from a common ancestral domain.
CDTree has been designed to discover and explore such relationships in detail, and is a central tool used to craft all of the curated domain hierarchies in the CDD.
Read more about CDD:
Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M,
He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki C, Liebert CA, Liu C, Lu F,
Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA,
Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a Conserved Domain Database for
protein classification.
Nucleic Acids Res. 2005;33 Database Issue:D192-6.
[Abstract]
[Full Text]
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