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This wiki page introduces know-how of Web API for Biology (WABI). Japanese page is here.

Contents 1 Keyword search 2 Retrieve entries 3 Homology search 4 NCBI Entrez Programming Utilities 5 ClustalW 6 Configure environment 7 Use proxy server 8 Use query including non alphanumeric character 9 Other know-how 10 Link

Keyword search

• Phrase search by ARSA
• AND OR search with plural keywords by ARSA
• Retrieve entries by specifying gene name
• Retrieve entries by specifying organism name
• Search DDBJ entries by gene name of human

Retrieve entries

• Retrieve entry by specifying sequence length against DDBJ database
• getDDJEntry of GetEntry service does not work
• Retrieve DDBJ entries by specifying gene name and execute BLAST at once
• Retrieve amino acid sequences of ORF whose organism is Herpes virus and whose length is over 50.
• Retrieve DNA sequence of DDBJ entry by specifying accession number
• Retrieve organism name of DDBJ entry by specifying accession number
• Retrieve genome entry of virus from DDBJ

Homology search

• Specify reference database same as DDBJ web page in BLAST
• Retrieve result with XML format from BLAST
• Retrieve reference database list of BLAST
• Execute BLAST with local DNA sequence file
• Execute BLAST with accession number
• Specify all DDBJ database for BLAST
• Shorten execution time of BLAST
• Extract specific organism from BLAST execution result
• Retrieve DDBJ entries by specifying gene name and execute BLAST at once
• Execute TBLASTN against large database
• Nr database of default cannot be specified against BLAST
• Execute BLAST asynchronously
• Examine the meaning of each column in the BLAST tab delimited format which is generated by -m 8 option.

NCBI Entrez Programming Utilities

• Search dbSNP by gene name of an acetaldehyde
• Retrieve genotype and frequency from SNP ID
• Search PubMed by Reference SNP ID
• Retrieve reference SNP ID that has an amino acid substitution from a protein ID
• Retrieve amino acid sequence and OMIM ID from a protein ID
• Retrieve OMIM record by OMIM ID
• Search OMIM by specified keyword
• Retrieve sequence details from ID that starts with "NM" or "NC"

ClustalW

• Execute ClustalW

Configure environment

• Solve java.lang.NoClassDefFoundError problem

Use proxy server

• Use REST service via a proxy server with LWP
• Use REST service via a proxy server with socket(Perl)
• Use REST service via a proxy server with URLConnection(Java)
• Use REST service via a proxy server with socket(Java)
• Use REST service via a proxy server with socket(C)
• Use REST service via a proxy server with socket(Ruby)
• Use REST service via a proxy server with socket(Pyhton)
• Use SOAP service via a proxy server with SOAP::Lite
• Use SOAP service via a proxy server with AXIS

Use query including non alphanumeric character

• Encode query with Perl
• Encode query with Java
• Encode query with C
• Encode query with C Sharp
• Encode query with Ruby
• Encode query with Python

Other know-how

• Retrieve version of Ensembl service
• Retrieve execution result of asynchronous method
• Construct SOAP server same as DDBJ
• Execution result cannot be retrieved.
• About the SOAP binding
• Prevent time-out
• SOAP is unavailable with SOAP::Lite 0.69
• Use SOAP with Ruby
• Error occurs in REST execution
• Use DDBJ services in Taverna
• Use DDBJ WebAPI in my service

Link

Japanese page