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Termination of a part of DDBJ services

DDBJ discontinues the following services provided by WWW and by E-mail, as of the described schedule. We apologize for your inconvenience. Thank you for your understanding and cooperation.

Services substitute services of DDBJ
Search & Analysis by E-mail server
  getentry 2008.9.12 (terminated) getentry (WWW *1 / WABI *2)
  get-version 2008.9.12 (terminated) getentry (WWW *1 / WABI *2)
  FASTA 2008.9.12 (terminated) FASTA (WWW *1 / WABI *2)
  BLAST 2008.9.12 (terminated) BLAST (WWW *1 / WABI *2)
  SSEARCH 2008.9.12 (terminated) SSEARCH (WWW *1
  ClustalW 2008.9.12 (terminated) ClustalW (WWW *1 / WABI *2)
  HMMPFAM 2008.9.12 (terminated) HMMPFAM by WWW*1
Keyword Search
  SRS 2008.12.26 ARSA==>Termination of SRS
Sequence Pattern Match
  SQmatch 2008.11.14  
Protein Compatibility Analysis, etc.
  PDB Retriever 2008.11.14  
  Libra 2008.11.14 GTOP
  Lib score 2008.11.14 

*1: Receiving the results by E-mail after sending the queries by WWW is continuously available.
*2:WABI stands for Web API for Biology and can be called by programs written by Perl, Java, C, Ruby and Python (ref: http://www.xml.nig.ac.jp/)

  
DDBJ terminated SRS (Sequence Retrieval System) service as of
December 26, 2008. Please use ARSA hereafter.

  

Termination of providing SRS(Sequence Retrieval System) services

DDBJ terminates providing SRS services (by WWW and WABI ) as of the December 26, 2008. We appreciate very much that you have used SRS since it was firstly launched in DDBJ in 1999. We apologize for your labor switching your keyword search system from SRS to ARSA, but, we hope ARSA is useful for all DDBJ users. Please refer the summary of ARSA and SRS shown in below.

(1) ARSA and SRS Search functions

               A R S A S R S
Search
 Engine
High-speed XML database search engine "Interstage Shunsaku" was applied for the nucleotide sequence database retrieval Keyword search system developed by EBI(European Bioinformatics Institute) was applied and reconstructed for the DDBJ database retrieval
Key Features
  • Rapid response: Even in any complex search keys, the results are returned within 5 seconds
  • In the DDBJ database retrieval, any combination of feature/qualifiers used in the DDBJ flat file format can be specified as search keys
  • Wide variety of WEB API programs such as SOAP/REST is applicable
  • From Quick Search (simple keyword search) to Advanced Search (specify a complex search queries), multistage search condition can be selectable.
  • Wide variety of WEB API programs such as SOAP/REST is applicable
functions ARSA SRS
Cross search of multiple DB  Yes   Yes 
Specifying the search field  Yes   Yes 
Use of DDBJ flat file Feature/Qualifier  Yes   No 
Quick search  Yes   Yes 
Multiple keywords connection using and/or/not Yes*  Yes 
Relation to analysis tools  Yes   Yes 
Speed fast slow

*: Use of "not" in Quick Search is in being enhanced (as of Aug. 2008)

(2) ARSA Improvement History

    No. of
DBs
2004.12 Trial operation started at the DDBJ HP
"DDBJ" and "DDBJNEW" only
 2 
2005.12 Upgraded
Full-time operation started
 
2007.02 21DBs other than DDBJ was added  23 
2007.07 Extensive Enhancement and transfer to Official Operation
<Main New Functions>
  • The search results can be downloaded across databases
  • Change of the displayed items in the result view screen is possible
  • API(Application Program Interface) for Java/Perl was enhanced
 
2007.10 DDBJ HP design renewal
(ARSA is available at the search window of DDBJ HP)
 
2007.10 Sequence search program linked to TX Search was changed from SRS to ARSA  
2007.11 Further Upgrade subsequent to enhancement conductted in July"
<Main new functions>
  • Addition of KEGG Pathway Database
  • Specification of detailed search conditions in the all databases, as well as DDBJ
  • Cross search by the common search queries
 24 
2008.05 Removal of redundant DBs
4DBs related to PFAM were removed
 20 

(3) Usage of ARSA and SRS

In the Page View count, ARSA exceeded SRS in March, 2008.

      srstoarsa_static
Unique User: a number of an individual that has visited a Web site or received specific content,for a specified period of time such as a day or month. More than one time visits by the same user is counted as 1.
Page View: a request to load a single page of an Internet site. This number is widely used as an access index to the site

(4) Conclusion

DDBJ, since starting the ARSA services in December of 2004 as a trial operation, has built up continuous improvements for the more convenient keyword search system. Meanwhile, DDBJ has introduced ARSA at the scientific meeting and DDBJing tutorials. The increase of ARSA users reflects these efforts, and as a result, DDBJ decided to terminate providing SRS service.

DDBJ will do all the more efforts for the development of ARSA. If you have any comments for ARSA, please send it from "Your Comment" which is located in the upper blue zone.

August 8, 2008