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Help Page : PeptideMine | Web Server for Identification & Analysis of Peptides from Interacting Proteins:

PeptideMine is a webserver developed for experimental and computational biologists interested in identifying and analysing peptides suitable for protein-peptide binding studies. PeptideMine is using a unique, knowledge based approach for the identification of peptides from the interacting sequence-space of a protein using different search programs (PeptideMine Search, BLASTP and regular expression based pattern). The peptides identified using the searches can be examined using different peptide related features. User can perform specific searches using different search programs with in the interacting partners of a given gene. Integrated GO annotations, protein-protein interaction data, peptide-domain mapping, domain-domain interaction data and various peptide related feature calculation provides a reliable approach to identify new peptides for protein-peptide binding studies.

PeptideMine Server - Help Index :
PeptideMine - Workflow Diagram:

1. Input Method - 1 - Submit Gene name:

PeptideMine is an integrated web server for the identification of peptides from interacting partners of a given protein based on different criteria. Using the main Server page, user can submit a job to PeptideMine server. For a succesful job submission to PeptideMine server using the 'Submit Gene Name' based input form, user should submit a valid Protein ID. Please note that PeptideMine is using Protein-Protein Interactions recorded in STRING database in the back-end to identify known and predicted interacting partners of a given protein. Currently PeptideMine is available for 6 genomes. Users should use the Protein IDs used to map interactions in the STRING Database. Please refer to the following table for the details about different genomes and their respective Protein IDs to be submitted to the PeptideMine Server. An alternative option is available to search gene-alias and automatically submit genes to PeptideMine based on the search result. This option is available with input Method -2.

OrganismID
Homo Sapiens Ensembl ID
Mus Musculus Ensembl ID
Caenorhabiditis Elegans Ensembl ID
Saccharomyces Cerevisiae Ensembl ID
Drosophila Melanogaster CG Number
Arabidopsis Thaliana TAIR ID


2. Input Method - 2 - Search for genes using 'Search & Submit' option:

Users can search the gene-alias database based on STRING alias file in the backend of PeptideMine server using different key words to identify genes of interest to submit in the PeptideMine Server. This allows novice users without the knowledge of specific IDs required for the PeptideMine Server to search using their key word of interest against specific genome-alias files and submit the respective Protein IDs to the PeptideMine Server. Users can access this option from the 'Search & Submit' link in the upper-panel of the server.


3. Details about various input options:

PeptideMine is an integrated webserver for the identification and analysis of peptides from interacting partners of a given protein, which can be used for protein-peptide binding studies. PeptideMine is using Protein-Protein Interactions recorded in STRING database in the back-end to identify known and predicted interacting partners of a given protein. Currently PeptideMine is available for 6 genomes. Users can perform the search to identify potential interacting partners using different criteria provided by the STRING database. For a successfull PeptideMine job submission, user should submit all the parameters.


3.1: Enter your valid email address:

Please submit your valid, preferably academic email address. Check your email address for any 'typos' before submitting to the server. We remind the users that "PeptideMine Server is using a computationally intensive protocol". We encourage users to submit their academic email address to the PeptideMine Server.


3.2: Select the organism:

PeptideMine server is using Protein-Protein Interactions recorded in STRING database in the back-end to identify known and predicted interacting partners of a given protein. Currently PeptideMine is available for 6 genomes. Users should select the organism of interest for the successful submission of PeptideMine job to the server. Users should select organims from the drop-down menu available in the 'Server' page and Search & Submit' page to get proper results.


3.3: Enter Protein ID:

For a succesful job submission to PeptideMine server using the 'Submit Gene Name' based input form, user should submit a valid Protein ID. Please note that PeptideMine is using Protein-Protein Interactions recorded in STRING database in the back-end to identify known and predicted interacting partners of a given protein. Currently PeptideMine is available for 6 genomes. Users should use the Protein IDs used to map interactions in the STRING Database. Please refer to the table in the section '1. Input Method - 1 - Submit Gene name' for organisms and their respective Protein IDs available in the current version of PeptideMine.


3.4: Select confidence score to identify interacting proteins from STRING (v 8) database:

PeptideMine server is using Protein-Protein Interactions recorded in STRING database in the back-end to identify known and predicted interacting partners of a given protein. Users can control the searches to identify interacting partners by selecting different confidence scores assigned to individual protein-protein interactions in the STRING database. Please refer the STRING papers for a better understanding of this scoring scheme. Users are encouraged to refer to the STRING help page and blog about the STRING confidence scores for more details. We are providing 4 different cut-offs of confidence score to identify interacting proteins for a given Protein ID from STRING database in the back-end.


3.5: Select prediction method to search for interacting proteins:

PeptideMine server is using Protein-Protein Interactions recorded in STRING database in the back-end to identify known and predicted interacting partners of a given protein. Users can control the searches to identify interacting partners by selecting different prediction methods used in the STRING. Users are encouraged to refer to the STRING help page and blog about the STRING for more details. We are providing 8 different methods available from the STRING database. Users can select any one of the 7 different prediction methods(Neighborhood, Gene Fusion, Co-expression, Experiments, Co-occurence, Databases, Textmining) or 'All method'(combined method of all 7 prediction methods) to identify the interaction. Interacting partners of a given gene is identified by searching the direct interacting partners (level 1, only binary interactions are considered in the current version) based on the selected Confidence score and prediction method. The search is performed in the local version of STRING database in the backend of PeptideMine server.


3.6: High-light interacting partners using GO-term:

PeptideMine server is using a unique approach to integrate predicted and known protein-protein interaction data from STRING with Gene Ontology. Along with the name and alias of the given interacting partner, users can also obtain the Gene Ontology annotations of the interacting partner in the results page of PeptideMine Server. This will help users to decide suitablity of peptides from a particular interacting partner can be used for the protein-peptide binding studies using insilico or invivo methods. Gene Ontology annotations of 6 genomes in the PeptideMine server is integrated using the BioMart based webservices. As GO annotations are highly informative, In PeptideMine we are providing an option for the user to high-light any GO-term / GO:ID among the available annotations of the the interacting partners of a gene. This will help the user to further analyse the peptides from genes with interesting GO annotations.


3.7: Switch off PSIPRED & DISOPRED predictions:

As a default option, PeptideMine server runs PSIPRED and DISOPRED in the backend for all interacting partners of a given gene. This is the most computatinal-intensive step in the PeptideMine workflow. This is a very useful approach that provides the user to get an idea about the secondary structure and disorder properties of different peptides identified by the search programs using query parameters. These predictions are run single time on the whole-sequence. If a user required faster results, we are providing an option to switch-off these predictions. By clicking on this check-box, users will get faster results depending up on the parameters used for interacting-partner search and number of already available jobs in the server.


3.8: Select the search program:

PeptideMine is an integrated web server designed and developed for the identification of peptides from a given gene's interacting partners for invitro and insilico protein-peptide binding studies. PeptideMine server is using Protein-Protein Interactions recorded in STRING database in the back-end to identify known and predicted interacting partners of a given protein. It also integrate Gene Ontology of genes along with Protein-Protein Interaction data. PeptideMine also offers assessment of peptides for protein-peptide binding studies based on different parameters (). PeptideMine offers three different search programs to search in the interactome-space of a given protein. Users can opt for any one of the three programs to perform their search depending up on the type of query and the context of the search.

The three different programs available from PeptideMine server are :
  • 1. PeptideMine Search:

    PeptideMine search is a simple pattern search program, that requires an amino acid residue and the desired length of peptide as input.This will be useful if the user is interested to obtain a list of peptides that contain a particular residue in desired length. This program retrieve all occurences of a peptides of given length that contains the particular residue. All instances are reported as the various parameters used to assess the peptides will change depending up on the difference in sequence.

  • 2. BLASTP Search:

    The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Along with 'PeptideMine search' PeptideMine also offers an option to perform BLASTP search against a database of interacting-partners of a given gene. This option requires the user to submit the sequence along with the E-value to perform BLAST searches. Usually peptides are of length in the range of 5-15 residues. PeptideMine is a server designed and developed for the identification and analysis of peptides from interacting proteins. Users may please avoid submitting larger sequences in the BLASTP search option provided in the PeptideMine server. This option will be highly useful for identifying peptidesbased on peptides available in the literature reports and can also help the users to identify homologs/orthologs of biologically active peptides from earlier reports.

  • 3. PROSITE pattern Search:

    PeptideMine Server scans every peptide identified by the server for PROSITE patterns to identify functional patterns based on ScanProsite. We also provide an option to perform PROSITE based pattern search to identify PROSITE patterns with in the interacting partners of a given protein. If users wanted to search using PROSITE based search, user should select this option. PROSITE pattern is the only input parameter with this mail.


3.9: Enter specific residue(s)/sequence/pattern to search in interacting proteins:

Users should submit query residue/residues/PROSITE pattern/short peptide sequence in the given text-box. Only residues/PROSITE patterns/sequence in raw format is allowed. No fasta format, Please. Please select the search program and provide the respective output. Server wont give proper output if you selected PeptideMine Search / BLASTP search and submitted PROSITE pattern as the input.


3.10.a: Select the size of peptide:

PeptideMine Search is the default search program in the PeptideMine server. The option 'Select the size of peptide' is associated with PeptideMine. As explained in ''Search Programs', the PeptideMine Search option requires two input parameters. Residue of interest and size of the peptide. Users can use the drop-down menu to set the size of the peptide. Currently the size can be set in the range of 9-15. This is a dynamic option, depending on the search program selected by the user, this option will change. This input parameter is only available with the


3.10.b: BLAST E-value:

The E-value or the expectation value is a statistical significance threshold for reporting matches against database of sequences. If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Increasing the threshold shows less stringent matches. This option is an input parameter of BLASTP search. Only if the user select the BLASTP search, this option will get enabled.


Contact:
Prof. R. Sowdhamini (Contact : mini@ncbs.res.in)
Prof. B. Gopal (Contact : bgopal@mbu.iisc.ernet.in)


PeptideMine - Team:
K. Shameer, LL Madan, S. Veeranna, Prof. B. Gopal & Prof. R. Sowdhamini