Pclust --- visualization of your protein network 
with emphasis on experimental studies

General Description and submission:
    Pclust is a web server, which provides a user-friendly interface to visualize an all-to-all pairwise similarity network (A2ApsN), placing emphasis on "reference proteins" and providing access to their full information available in source databases, e.g. articles in PubMed. 
    The ease of cross-database linkage and the identification of "reference proteins" will facilitate understanding the functions of protein clusters in the network, thus promoting the interpretation of your proteins of interest. Pclust has four modes; a user can specify input as 1) a single sequence, 2) multiple sequences, 3) a Seq2Ref result link, and 4) customized network data. (formats explained here). The flow chart for each mode is available by clicking the links. The four above modes are designed to provide networks 1) for any single sequence, 2) with an advanced interface similar to CLANS, 3) for previously generated Seq2Ref jobs, and 4) with a customized input that grants users the flexibility to design.  

Submission:
    To submit a job to Pclust, you must provide your email address and one of the three acceptable formats (described below). Once the job is done, an email containing the link to the result page will be sent to you. 


Terms in the input interface:

1. Input email (required): 
when your job is done, your result will be sent to this email address.

2. Input job name: Assign an optional name to identify your Pclust job. This name will appear in the subject line of the email sent to you.

3. BLAST parameters: There are three parameters used in the BLAST search.
    3.1 Expect threshold (aka e-value): Expected number of matches in a random model. Smaller e-value indicates higher statistical confidence. Detailed explanation at http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect
    3.2 Number of PSI-BLAST iterations: If 1 iteration is specified, then BLASTP will be run. Otherwise, Pclust will run PSI-BLAST with the iteration indicated (weblink to psi-blast).
    3.3 Max target sequences: Maximum number of aligned sequences contained in the BLAST result and to be considered in detecting reference proteins by the Seq2Ref server.
       
4. Fetching Pubmed literature: The retrieval of reference proteins linked to Pubmed literature requires searching NCBI databases using the Seq2Ref server. Seq2Ref can perform this search in one of two modes, fast mode or slow mode.

    4.1 Fast mode: reference proteins and Pubmed articles are retrieved by searching a local database that we update every six months. With the default parameters, jobs will take 5--10 min to complete. The drawback of fast mode is that Pubmed articles newer than six months will be missed.
    4.2 Slow mode: reference proteins and Pubmed articles are retrieved directly from the NCBI servers via Entrez. With the default parameters, jobs will take about an hour to complete. Slow mode fetch ensures the most current set of reference proteins and Pubmed articles are retrieved.


5. Identity cutoff for clustering: This cutoff for pairwise identity between proteins is used in the CD-HIT program to reduce the redundancy of the protein set. The default cutoff is 0.95 (95% identity).

Terms in the server result page:

1. Score: this score is taken from Seq2Ref server. Please refer to Seq2Ref documentation.

2. Expect threshold or e-value: For BLAST results, expected number of hits in a random model. Detailed explanation refers to: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect

3. Identities: The percent amino acid identity between the query and target proteins calculated by taking the ratio of the identical positions to the total aligned positions in the alignment.

4. Coverage: The extent to which the aligned sequence region covers the full sequence length in an alignment, often expressed as a percentage. Coverage is calculated by taking the ratio of the non-gap aligned region to the longest protein sequence in the alignment.
    
5. Iteration: the number of PSI-BLAST iterations run. This parameter will be hidden if set to 1 in the input.

6. Pubmed: All publication(s) that NCBI has associated with a protein.

7. The evidence code: this code is taken from the Seq2Ref server. Please refer to here.

8. Reference(s): The output shows full citations for all literature references associated with each reference protein. The citations are sorted by date. For references with more than 10 authors, only the first five and last five authors are listed.

9. Positives: The extent to which two sequences share residues with similar biochemical properties in an alignment. Positives are calculated by dividing the number of positions that contain a positive-scored residue pair in the BLOSUM matrix by the alignment length. 

10. Gaps: The fraction of the alignment that is composed of gaps.

11. Functional annotation: The function of a reference protein, as described in the 'General annotation (Comments)' section of the Swiss-Prot database record.


Other vocabulary:

1. reference proteins: proteins with either experimental studies or manual curations; Their function interpretations are supported by expermental data and not origniated from automatic annotation transfer.

2. BLOSUM (BLOcks of Amino Acid SUbstitution Matrix) matrix: The substitution matrix used for sequence alignment of proteins. Details refer to http://en.wikipedia.org/wiki/BLOSUM