Difference between revisions of "HSSP curve"

From Protein Prediction 2 Winter Semester 2014
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== Existing visualisations ==
+
= Existing visualisations =
   
   
== Core Functionalities ==
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= Core Functionalities =
- Import BLAST results
 
- Parse BLAST results
 
- Visualize HSSP curve
 
- Filter HSSP curve based on a threshold
 
 
= Progress =
 
 
 
<div style=" text-align:left; width: 60% ; overflor:auto; height:10em border:2px">
 
<div style=" text-align:left; width: 60% ; overflor:auto; height:10em border:2px">
 
{| class="wikitable"
 
{| class="wikitable"
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! scope="col" width="70%" | Task !! scope="col" width="30%" | Implemented
 
! scope="col" width="70%" | Task !! scope="col" width="30%" | Implemented
 
|-
 
|-
| Core Functionality || No
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| Import BLAST results || No
|-
 
| Drag nodes || No
 
|-
 
| Display additional info on mouse-over || No
 
 
|-
 
|-
| Edit graph and export changes || No
+
| Parse BLAST results || No
 
|-
 
|-
| PBseq format compatibility || No
+
| Visualize HSSP curve || No
 
|-
 
|-
| Connect (.ct) format compatibility || No
+
| Filter HSSP curve based on a threshold || No
 
|}
 
|}
 
</div>
 
</div>
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* [mailto:agon.lohaj@gmail.com Agon Lohaj]
 
* [mailto:agon.lohaj@gmail.com Agon Lohaj]
   
== References ==
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= References =
   
 
http://en.wikipedia.org/wiki/Homology-derived_Secondary_Structure_of_Proteins
 
http://en.wikipedia.org/wiki/Homology-derived_Secondary_Structure_of_Proteins

Revision as of 11:41, 20 November 2014

Introduction to HSSP curve?

HSSP is a derived database merging structural (3-D) and sequence (1-D) information. For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). The database is updated frequently. The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures covering 29% of all SwissProt-stored sequences.


Different thresholds for HSSP-curve
Different thresholds for HSSP-curve


Existing visualisations

Core Functionalities

Task Implemented
Import BLAST results No
Parse BLAST results No
Visualize HSSP curve No
Filter HSSP curve based on a threshold No

People

References

http://en.wikipedia.org/wiki/Homology-derived_Secondary_Structure_of_Proteins

http://www.ncbi.nlm.nih.gov/pubmed/?term=UniqueProt%3A+creating+representative+protein+sequence+sets

http://en.wikipedia.org/wiki/Protein_superfamily

http://nar.oxfordjournals.org/content/24/1/201.full.pdf