Difference between revisions of "DASworkshop200802:spice"
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=SPICE= | =SPICE= | ||
==a browser for protein sequences, structures and their annotations== | ==a browser for protein sequences, structures and their annotations== | ||
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There are various ways to launch SPICE. | There are various ways to launch SPICE. | ||
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notice how the PFAM track is on top of the UniProt display. | notice how the PFAM track is on top of the UniProt display. | ||
map the PFAM domains on the structure. | map the PFAM domains on the structure. | ||
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| + | ==A multiple structure alignment viewer== | ||
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| + | ===CASP 7 results=== | ||
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| + | The [http://www.predictioncenter.org/casp/casp7/public/cgi-bin/results.cgi CASP 7 - target view] allows to launch SPICE again | ||
| + | |||
| + | white... solved target. | ||
| + | others: predictions for various targets. | ||
| + | sort predictions by score | ||
| + | switch between sequence based on structure based alignment algorithms. | ||
Revision as of 13:36, 24 February 2008
Contents
SPICE
a browser for protein sequences, structures and their annotations
There are various ways to launch SPICE.
Ensembl
The PDB_Spice DAS track in the Ensembl protview and contigviews allows to show protein structure mappings/
e.g. http://www.ensembl.org/Homo_sapiens/protview?peptide=ENSP00000365116
enable the track in this view and click on the track and then again on the protein structure image. This allows you to launch SPICE.
Pfam
SPICE can be easily linked to from external web sites.
Find the protein structure 1cdg in Pfam: http://pfam.sanger.ac.uk/structure?entry=1cdg&type=Structure
click on view structure and select SPICE again.
notice how the PFAM track is on top of the UniProt display. map the PFAM domains on the structure.
A multiple structure alignment viewer
CASP 7 results
The CASP 7 - target view allows to launch SPICE again
white... solved target. others: predictions for various targets. sort predictions by score switch between sequence based on structure based alignment algorithms.
