Help & FAQs

» Help

» Mandatory requirements

All the files submitted to the webtool MUST:

  • Be in plain text (e.g. ".doc" or ".rtf" files are not accepted ).
  • Have only one column with the gene names (one gene name per line).

» Database: Organism

This interface allows users to access to the database in an intuitive and user friendly manner.

How to use the Full organism search tool:

  • Select the organism.
  • Choose the programs to use in the query. You can perform a full search with the default cut-off values, or construct a customized search..
  • Define the cut off values to be assigned to the selected tools (click here to read about the different cut-off values).
  • (Optional) Apart from the basic analysis, you can select and perform an extra analysis by choosing the “Pfam domain screening” option.
  • Select the results format:
    • ID List: to obtain a list with the identifiers of the predicted proteins
    • FASTA file: to obtain a FASTA file with the sequences of the predicted proteins
    • Both: to obtain both sorts of files, the ID list and the FASTA file.
  • (Optional) Enter an e-mail address to receive a message with the link to download the results. Otherwise, you can download them from the link displayed on the screen.
  • Submit to start search

A description of the results obtained from this query is included in the appropriate section at the end of this manual.

pipeline

Available interface for the Full Organism search.

» Database: Query user

Through this interface, the user can retrieve information related to a set of specific proteins of interest from the database.

How to use the User query search tool:

  • Select the organism of interest.
  • Choose the kind of feature to be queried. It may differ depending on the organism.
  • Paste the identifiers into the text box or upload a text file with a list of identifiers.
  • Choose the programs to use in the query. You can perform a full search with the default cut-off values, or construct a customized search.
  • Define the cut off values to be assigned to the selected tools (click here to read about the different cut-off values).
  • (Optional) Apart from the basic analysis, you can select and perform an extra analysis by choosing the “Pfam domain screening” option.
  • Select the results format:
    • ID List: to obtain a list with the identifiers of the predicted proteins
    • FASTA file: to obtain a FASTA file with the sequences of the predicted proteins
    • Both: to obtain both sorts of files, the ID list and the FASTA file.
  • (Optional) Enter an e-mail address to receive a message with the link to download the results. Otherwise, you can download them from the link displayed on the screen.
  • Submit to start search.

A description of the results obtained from this query is included in the appropriate section at the end of this manual.

pipeline

Available interface for the User Query search.

» BLAST search

Through this interface, the user can access our database to obtain the orthologs matching their proteins of interest.

How to use the Local BLAST search tool:

  • Paste the identifiers to be analyzed into the text box or upload a text file with a list of identifiers.
  • Select the dataset to be considered in the BLAST analysis from the list below:
    • Non Refined Predictions Set (NRPS)
    • Non Refined Predictions Curated Set (NRPCS)
    • Refined Predictions Set (RPS)
    • Non Refined Predictions Curated Set (RPCS)
  • Select the BLAST algorithm.
  • Define the cut-off value or use the default (click here to read about the different cut-off values).
  • (Optional) Enter an e-mail address to receive a message with the link to download the results. Otherwise, you can download them from the link displayed on the screen
  • Submit to start search.

A description of the results obtained from this query is included in the appropriate section at the end of this manual.

pipeline

Available interface for the Local BLAST search.

» Downloads

Using this interface, the user can get a set of downloadable files, including the different sets of secreted proteins (as predicted) for any of the organisms in the database. This way, it is possible to obtain the data from an individual genome or bulk database predictions using the provided links. The different sets of proteins predicted as secreted are:

  • Non Refined Predictions Set (NRPS)
  • Non Refined Predictions Curated Set (NRPCS)
  • Refined Predictions Set (RPS)
  • Non Refined Predictions Curated Set (RPCS)

To obtain the desired files, the user must right-click on the suitable link and choose where to save the provided zip file.

pipeline

Available interface to download the different pools of proteins predicted as secreted for any of the considered organisms.

Caution: Due to the limited UniProt availability of curated datasets, the Non Refined Predictions Curated Set (NRPCS) or the Non Refined Predictions Curated Set (RPCS) are not available for all listed organisms.

» Results

» Full organisms search

After requested analyses have been performed, the obtained results are organized in two parts:

  • The first part is a sortable table that shows the lists of proteins obtained from the database query with associated data. Each protein name is linked to a webpage where more comprehensive information is available.

    pipeline

    Sortable table of the obtained results.

    This table in Excel format, as well as the requested results (ID list, FASTA file or both) and the cutoffs used in the query, can be downloaded using the available link (within a red circle in the below picture).

    pipeline

    Link to download the zip file.



    pipeline

    Example of the zip file that can be downloaded from this link.

  • The second part is a webpage where data are presented for each specific predicted protein (see screenshots below):
    • A table with different identifiers for the gene that encodes the predicted protein and proper links to the original databases.
    • A second table that contains the values of the prediction parameters.
    • A third table with the curated data related to the protein.
    • Representation of the protein transmembrane domain structure through a link to the tool "Protter".
    • A table concerning “Structural domains” including InterPro domains and their related Gene Ontology (GO) identifiers.
    • A schematic representation of the domain structure.
    • The FASTA sequence of the protein.
    • A graphic detailing protein-protein interactions from STRINGDB.
    • Links to the results that are detailed in the "Downloadable results" section.

    pipeline

    Example of the webpage where we present the data of a protein predicted as secreted.

    As in the previous case, all of the mentioned results can be easily downloaded using the links provided at the bottom of the page:

    • The upper one retrieves the protein-protein interaction table
    • The lower one retrieves the tables and images presented in the webpage.

    pipeline

    Link from which download the table obtained from the queries launched to our database.

    The results available using this lower link are provided into a compressed zip file, which contains:

    • Curation.txt: a file that contains a table with the curated data from Uniprot.
    • InterPro.txt: a file that contains a table with the InterPro domains and the GO identifiers.
    • predictionParameters.txt: a file that contains all the values of the prediction parameters for the specific protein.
    • sequence.fa: sequence in FASTA format of the protein.
    • sequenceIDs.txt: a file that contains a table with the different identifiers that correspond to the gene which encode for the protein.
    • Protein_Name.png: a diagram of the protein domains calculated by InterPro.
    • PPinteraction.jpg: a diagram of the interactions between proteins.

    pipeline

    Example of the zip file that can be downloaded and the enclosed documents.

» User query search

The results that are obtained from the User query search are shown in the same way than the ones described for the Full organism search.

» Local BLAST

BLAST results in plain text (BLAST format 7) are shown in the webpage and can be downloaded through the link shown at the beginning of the same page.

pipeline

Example of the webpage in which results obtained from a BLAST search are ouput.

pipeline

Example of the zip file that can be downloaded from the above mentioned link.