Protonet: Hierarchical Classification of the Protein Space
The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for mer...
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| Main Authors: | , , , , , , |
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| Format: | text |
| Language: | English |
| Published: |
Institutional Knowledge at Singapore Management University
2003
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| Subjects: | |
| Online Access: | https://ink.library.smu.edu.sg/sis_research/88 http://dx.doi.org/10.1093/nar/gkg096 |
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| Institution: | Singapore Management University |
| Language: | English |
| Summary: | The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a hierarchy of clusters of varying degrees of granularity. ProtoNet (version 1.3) is accessible in the form of an interactive web site at http://www.protonet.cs.huji.ac.il. ProtoNet provides navigation tools for monitoring the clustering process with a vertical and horizontal view. Each cluster at any level of the hierarchy is assigned with a statistical index, indicating the level of purity based on biological keywords such as those provided by SWISS-PROT and InterPro. ProtoNet can be used for function prediction, for defining superfamilies and subfamilies and for large-scale protein annotation purposes. |
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