Below is additional information that could help you with issues or questions you may have.
About HPIDB 3.0
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Search By Sequence
A sequence based(blastp) search of HPIDB. The user can input a single sequence or a file of protein sequences in FASTA format. A sample input file is given here. The user can select a database of choice and modify BLAST options(E-value, percent identity, query_coverage, number of hits to return). The BLAST results are provided in both tabular format and alignment format (standard BLAST output file). The percent_identity and query_coverage criteria along with the E-value criteria will be used to filter the HPIDB interaction information and the GO information for the BLAST hits.
Search By Keyword
Select identifier type (like accession, symbol, taxonomy, publication id, author name, interaction type) to search the database and enter the desired identifier in the text box.
The search is implemented as a regular expression. Therefore, searches with partial information for the identifier are supported.
For example, select identifier type as Accession/Symbol and enter "Q16543" or "hspA" in the search box. Alternatively, select identifier type as Taxon and enter "10633" (taxon id) or "Influenza A virus" in search box to search HPIDB. Select identifier type as Publication (PMID or Author Name) and enter "20711500" (pmid) or "Dyer" (author_name) in search box to search HPIDB.
The output containing all HPI for hspA or Influenza A virus is generated as a table with 10 columns. These ten columns represent unique identifier ids for the two interacting proteins, taxonomy, detection method, interaction type, pubmed id, and source database. This table is a partial result and the full 26 column output described above (in the database schema section) can be downloaded in a psi-mitab format.
Search By Homologous HPI
For a given set of host and pathogen proteins, this module will search for homologous HPI, if available, in HPIDB (based on BLAST). The user can inspect the identified HPI dataset and assess the transferability of these interactions for functional modeling. This module requires different input files for different search strategies.
- For a given set of pathogen proteins search for homologous interactions in HPIDB, required input files are for only Form A. Sample input File pathogen sequences. Here is the sample output. The output lists the Query pathogen, the homolgous pathogen protein and the interacting host proteins.
- For a given set of host proteins search for homologous interactions in HPIDB, required input files are for only Form B. Sample Input File host sequences. Here is the sample output. The output lists the Query host, the homologous host protein and the interacting pathogen proteins.
- For a given set of host and pathogen proteins, search for homologous HPI interactions in HPIDB, required input files are for both Form A and Form B. Sample input File pathogen sequences and host sequences. The output lists the Query host, query pathogen, and the homologous host and pathogen proteins..
A 4 column unique interacting protein output file(tab delimited) can be used for further analysis in Cytoscape or any network visualization and analysis software. Example of 4 column unique interacting protein output(tab-delimited) file.
Uploading file in Cytoscape - Users can import 4 column tab-delimited unique interaction output file in cytoscape by following procedure.
Open cytoscape -> Select File -> import ->Network from table -> In input file (Select file option), select the file you just downloaded -> Click : Show test File Import option -> make sure only Tab option is checked (uncheck others) -> In Attributed Names Click : Transfer first line as attribute names -> In Intercation definition area select Source interaction as Column 1 and select Target interaction as Column 3 -> Click import (below right corner) -> When the network is loaded a message box appears as "Successfully loaded network ...", close it.
Here the network is loaded for you. You may change the layout as Layout -> yFiles -> Organic.
Similarly you can load node and edge attributed from the tab delimited files. More details are present in links given below.
Click here to read all option to import Network from Tables.
Click here to read all option to import Node and Attribute Edges from Tables.
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