Difference between revisions of "DASworkshop200802:spice"
(New page: =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 an...) |
(→A browser for protein sequences, structures and their annotations) |
||
| (14 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| + | back to the [[DASworkshop200802|DAS workshop page]] | ||
| + | |||
=SPICE= | =SPICE= | ||
| − | |||
| + | There are 2 main display modes in SPICE. | ||
| + | As a single protein structure browser and as a multiple protein structure alignment viewer. | ||
| + | ==A browser for protein sequences, structures and their annotations== | ||
There are various ways to launch SPICE. | There are various ways to launch SPICE. | ||
| Line 14: | Line 18: | ||
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. | 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. | ||
| + | |||
| + | Find the hsa35pep DAS track in the Ensembl peptide display. | ||
| + | |||
| + | Map the exon structure onto 3D. | ||
| + | |||
| + | Map the nsSNPs onto 3D. | ||
===Pfam=== | ===Pfam=== | ||
| Line 20: | Line 30: | ||
Find the protein structure 1cdg in Pfam: | Find the protein structure 1cdg in Pfam: | ||
| − | http://pfam.sanger.ac.uk/structure?entry= | + | http://pfam.sanger.ac.uk/structure?entry=1boh&type=Structure |
click on view structure and select SPICE again. | 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. | ||
| + | |||
| + | Do the PFAM domains correspond to what you would consider structural domains? | ||
| + | |||
| + | Find the hydrophobicity DAS source. (in the UniProt display, very much at the bottom) | ||
| + | map the Kyle-Doolittle hydrophobicity onto the protein structure. | ||
| + | |||
| + | === SPICE & histogram style data === | ||
| + | |||
| + | examples for how to display histogram style plots in SPICE can be see from here: | ||
| + | [http://www.efamily.org.uk/software/dasclients/spice/histogram.shtml http://www.efamily.org.uk/software/dasclients/spice/histogram.shtml] | ||
| + | |||
| + | |||
| + | === SPICE homepage === | ||
| + | |||
| + | Just for completeness, you can of course also launch SPICE via its homepage at | ||
| + | [http://www.efamily.org.uk/software/dasclients/spice/ http://www.efamily.org.uk/software/dasclients/spice/] | ||
| + | |||
| + | ==A multiple structure alignment viewer== | ||
| + | |||
| + | ===CASP 7 results=== | ||
| + | |||
| + | The [http://www.predictioncenter.org/casp/casp7/public/cgi-bin/results.cgi CASP 7 - target view] allows to launch SPICE in the structure alignment mode | ||
| + | |||
| + | white... solved target. | ||
| + | |||
| + | others: predictions for various targets. | ||
| + | |||
| + | sort predictions by score | ||
| + | |||
| + | switch between sequence based on structure based alignment algorithms. | ||
Latest revision as of 11:31, 26 February 2008
back to the DAS workshop page
Contents
SPICE
There are 2 main display modes in SPICE. As a single protein structure browser and as a multiple protein structure alignment viewer.
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.
Find the hsa35pep DAS track in the Ensembl peptide display.
Map the exon structure onto 3D.
Map the nsSNPs onto 3D.
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=1boh&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.
Do the PFAM domains correspond to what you would consider structural domains?
Find the hydrophobicity DAS source. (in the UniProt display, very much at the bottom) map the Kyle-Doolittle hydrophobicity onto the protein structure.
SPICE & histogram style data
examples for how to display histogram style plots in SPICE can be see from here: http://www.efamily.org.uk/software/dasclients/spice/histogram.shtml
SPICE homepage
Just for completeness, you can of course also launch SPICE via its homepage at http://www.efamily.org.uk/software/dasclients/spice/
A multiple structure alignment viewer
CASP 7 results
The CASP 7 - target view allows to launch SPICE in the structure alignment mode
white... solved target.
others: predictions for various targets.
sort predictions by score
switch between sequence based on structure based alignment algorithms.
