 CDTree: a protein domain hierarchy viewer and editor |
| 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
 Features added in CDTree 3.1
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Mac OSX
supported CDTree and Cn3D have been
ported to Macintosh computers running OSX
10.4 and higher
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Annotation matrix
Viewer conveniently record
and review annotations and literature
references for all domains in a hierarchy
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Multi-CD
operations new select and edit
operations that can act across multiple
domain models
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Sequence tree
coloring greater flexibilty in
visualizing evolutionary relationships between
domains
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Speed improvements optimized
computations to improve response time in
large domains and hierarchies
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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 and CDTree:
Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L,
He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F,
Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH.
CDD: a conserved domain database for interactive domain family analysis.
Nucleic Acids Res. 2007;35 (Database Issue):D237-40.
[Abstract]
[Full
Text @ PubMed Central]
[Full Text]
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