Difference between revisions of "HSSP curve"
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− | + | = Existing visualisations = |
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− | + | = Core Functionalities = |
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− | - Import BLAST results |
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− | - Parse BLAST results |
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− | - Visualize HSSP curve |
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− | - Filter HSSP curve based on a threshold |
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− | = Progress = |
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<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"> |
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{| 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 |
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+ | | Import BLAST results || No |
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− | | Drag nodes || No |
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− | |- |
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− | | Display additional info on mouse-over || No |
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− | | |
+ | | Parse BLAST results || No |
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− | | |
+ | | Visualize HSSP curve || No |
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+ | | Filter HSSP curve based on a threshold || No |
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</div> |
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* [mailto:agon.lohaj@gmail.com Agon Lohaj] |
* [mailto:agon.lohaj@gmail.com Agon Lohaj] |
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− | + | = References = |
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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 12:41, 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.
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