SPPS : Sequence-based Protein Partner Search  
Introduction   Query One   Query Two   Result   Document   Forum

Docoument

Users are free to use the SPPS server, including access to explore known protein partners. The user may provide his/her email address to receive the result or choose "anonymous" button to browse the result online. To launch a job, user should directly input a query protein sequence in the Query Frame ("Query One" module or "Query Two" module) and retrieve the result in the "Result" module when the job is finished.  User also can check the running status of the job by "Job queue status <http://www.dddc.ac.cn/spps/queue_status.php> " link at the bottom of the page.

Query One Module

Example1

In the mode, user can search for the candidate protein partners in specific species. User should provide one query protein sequence in FASTA format, and then choose a species database, finally submit the job. A job identity number, the ‘job_id’, is assigned to each job by the web server, and the number is appended to a job queue in the back-end server. The user may use the job_id to check the status of his/her job. When job is finished, the output file is created. The archive file contains a list of the scores, together with the Swiss-Prot accession number of protein partner hits, which is sent to registered email address of users as well as achieved as a copy for further possible analysis (Result module) ATTENTION: protein with more than 150 amino acids is suitable for the algorithm.

Query Two Module

Example2

In the mode, SPPS provide a tool to quickly evaluate whether two proteins are interactive based on the score of probability. User should provide two query protein sequences in FASTA format, and then choose a species, finally submit the job. By default, the predcited interaction between Query1 and Query2 is direct. If check box "consider indirect interaction?" is selected, indirect interaction between Query1 and Query2 linked by one or/and two intermediated proteins can be predicted. A job identity number, the ‘job_id’, is assigned to each job by the web server, and the number is appended to a job queue in the back-end server. The user may use the job_id to check the status of his/her job. When job is finished, the output file is created. The archive file contains a score for these two protein interaction, which is sent to registered email address of users. ATTENTION: proteins with more than 150 amino acids are suitable for the algorithm.

Result Module

In Query1_mode, the archive file contains a list of the scores, together with the Swiss-Prot accession number of protein partner hits. Optionally, user can analyze protein partner hits with several filters in the SPPS web server:

  • ‘Probability (P, 1>P>0) Match’ shows the protein partner hits ranging between two boundaries.
  • ‘Sequences with the following annotations available’ provide several filters to refine the protein partner hits.
  • The ‘Function’ filter refines protein partner hits with known function;
  • The ‘Disease’ filter refines protein partner hits relevant to known diseases;
  • The ‘Tissue specificity’ filter refines protein partner hits distributed with known tissue specificity;
  • The ‘Interaction’ filter highlights protein partner hits with known interaction;
  • The ‘Subcellular Location’ filter refines protein partner hits with known subcellular location.
  • ‘Tissue Match’ filter refines protein partner hits with the same tissues distribution as query protein.
  • ‘Known interaction’ filter highlights protein partner hits with known interaction to the query protein by specific label.
  • ‘Protein Partner Interaction Network Graph’ displays the predicted network graph extended from the query protein, which is supported by Java virtual machine and bioverse package. In the page of network, alll connections were validated by experiments, except predicted connections between "Query" and its partners. A typical graph view consists of a toolbar and a graph window. The toolbar contains a search field, freeze option (which stops the relaxation layout algorithm), drop-down functional annotation menu, distance selector (distance from selected node), screen refresh button, and total node/edge count. ‘Search’ can be performed by typing in the exact node label you're looking for (the query protein is named ‘Query’), or by using a wildcard asterisk  character. Note that wildcarding can only be used following a specific character, and only once per search term. If the search fails, a random set of nodes will appear. If no matches are found, a message indicating "No match" will appear in the search field. Search terms are case-sensitive. Using the left mouse button, select a specific node. It will turn green. All neighboring nodes up to a distance selected will highlight as yellow. Nodes outside of this neighborhood will be gray. Undirected edges with weights will appear according to a color code where green denotes the highest confidence, red denotes the lower, and orange and yellow denote intermediate confidences. A drop-down menu to select only proteins in particular functional category is available. Graph navigation can begin as before. For detailed information about bioverse package, you can visit the original site of bioverse in Washington: http://bioverse.compbio.washington.edu/viewer/
  • ‘Result’ outputs a refined result table by above filters.

In Query2_mode, the archive file contains a list of the directly and indirectly interactive scores, together with the Swiss-Prot accession number of intermediated proteins hits. User can view the result in the SPPS web server:

Reference

1. Juwen Shen, Jian Zhang et al. Predicting protein-protein interactions based only on sequences information Proc.Natl.Acad.Sci.USA 2007,104(11):4337-4341.

 

Statistics
Human Protein Entries 19,331
  Protein-Protein Interactions 16,443
  Accuracy(%) 83.9
     
C.elegans Protein Entries 2,860
  Protein-Protein Interactions 4,011
  Accuracy(%) 76.0
     
Drosophila Protein Entries 2,388
  Protein-Protein Interactions 21,999
  Accuracy(%) 78.1
     
Yeast Protein Entries 15,213
  Protein-Protein Interactions 15,517
  Accuracy(%) 81.8

News
  • 2006.5 SPPS launched
  • 2006.5 SPPS Database Updated
  • 2006.6 Human Model was added
  • 2006.8 Drosophila Model was added
  • 2006.9 C.elegans Model was added
  • 2006.11 Yeast Model was added
  • 2006.12 Database Updated
  • 2007.1 Indirect Interaction was added
  • 2008.1 Database Updated
  • 2009.3 Database Updated
  • 2010.1 Database Updated
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    Job queue status
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