Difference between revisions of "SkyBase"
(→‎SkyBase in geWorkbench)
Line 16: Line 16:
  
  
 +
After query with the sequence for PDB file 1e09:
 +
 +
 +
[[Image:SkyBase_1e09_full_normal.png]]
 +
 +
 +
Detail, upper left
 +
 +
 +
[[Image:SkyBase_1e09_upper_left.png]]
 +
 +
 +
 +
Detail, upper right
 +
 +
[[Image:SkyBase_1e09_upper_right.png]]
 +
 +
 +
 +
VAT page
 +
 +
 +
[[Image:SkyBase_1e09_VAT.png]]
 +
 +
 +
VAQ page
 +
 +
 +
[[Image:SkyBase_1e09_VAQ.png]]
  
 
=References=
 
=References=

Revision as of 17:30, 13 June 2011

Home | Quick Start | Basics | Menu Bar | Preferences | Component Configuration Manager | Workspace | Information Panel | Local Data Files | File Formats | caArray | Array Sets | Marker Sets | Microarray Dataset Viewers | Filtering | Normalization | Tutorial Data | geWorkbench-web Tutorials

Analysis Framework | ANOVA | ARACNe | BLAST | Cellular Networks KnowledgeBase | CeRNA/Hermes Query | Classification (KNN, WV) | Color Mosaic | Consensus Clustering | Cytoscape | Cupid | DeMAND | Expression Value Distribution | Fold-Change | Gene Ontology Term Analysis | Gene Ontology Viewer | GenomeSpace | genSpace | Grid Services | GSEA | Hierarchical Clustering | IDEA | Jmol | K-Means Clustering | LINCS Query | Marker Annotations | MarkUs | Master Regulator Analysis | (MRA-FET Method) | (MRA-MARINa Method) | MatrixREDUCE | MINDy | Pattern Discovery | PCA | Promoter Analysis | Pudge | SAM | Sequence Retriever | SkyBase | SkyLine | SOM | SVM | T-Test | Viper Analysis | Volcano Plot


Overview

SkyBase is a database that stores the homology models built by SkyLine analysis for all NESG PSI2 protein structures. Users can search the database with their sequence of interest to find homology models which meet user-defined alignment coverage and sequence identity constraints.

SkyBase Tutorial

http://skybase.c2b2.columbia.edu/nesg3/help/help.html


Database Search Page

http://skybase.c2b2.columbia.edu/nesg3/nesg.php


SkyBase in geWorkbench

After query with the sequence for PDB file 1e09:


SkyBase 1e09 full normal.png


Detail, upper left


SkyBase 1e09 upper left.png


Detail, upper right

SkyBase 1e09 upper right.png


VAT page


SkyBase 1e09 VAT.png


VAQ page


SkyBase 1e09 VAQ.png

References

Lee H, Li Z, Silkov A, Fischer M, Petrey D, Honig B, Murray D. (2010) High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. J Struct Funct Genomics. 11(1):51-9. Link to paper

Mirkovic N., Li Z., Parnassa A., Murray D. (2007) Strategies for High-Throughput Comparative Modeling: Applications to Leverage Analysis in Structural Genomics and Protein Family Organization. Proteins: Structure, Function, and Bioinformatics 66:766-777.

Retrieved from "http://wiki.c2b2.columbia.edu/workbench/index.php?title=SkyBase&oldid=8799"