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PubCrawler - an update alerting service for PubMed and GenBank

PubCrawler is a free "alerting" service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases.  PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests.


white ball Sample results page See an example of what PubCrawler does
white ball PubCrawler WWW-Service Run your GenBank and Medline searches on our server.
Get your results daily as a Web page or by e-mail.
white ball PubCrawler stand-alone Program For professionals: 
Install a copy of the PubCrawler program on your own computer (PC/Mac/Unix)


PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user.  There is no limit on the number of searches that can be carried out.  Previous search hits are stored and only the newest PubMed or GenBank records are shown each day.  The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query.  This Web page can be located on our computer (the PubCrawler WWW-Service), on your computer (the stand-alone program), or you can receive it via e-mail (set this up using the PubCrawler WWW-Service). The Web page sorts the results into groups of PubMed/GenBank entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit.

PubCrawler was developed by Karsten Hokamp and Ken Wolfe in the Department of Genetics, Trinity College Dublin, Ireland. The public web service has been in use since March 1999.

PubCrawler in the news:
  • PubCrawler was mentioned in the 'Netlines' section of the BRITISH MEDICAL ASSOCIATION (BMJ. 2000 Jul 29;321(7256):306B). This article is available online.
  • PubCrawler was featured as "Hot Pick" in the NetWatch page in January 14th issue of Science (Science 287:187c 2000)
  • An article about the PubCrawler WWW-Service appeared in the November 1999 issue of Trends in Genetics, Vol 15 No 11, 471-472 (full text available)
  • An online article about PubCrawler in EMBnet.news Vol 6_1

Other free alerting services:

PubCrawler looks for matches to text (Medline and GenBank annotation), not sequences, and writes its output as a WWW page.  Other "alerting" services scan sequence databases either for text or sequence similarity (BLAST) matches, and report by e-mail:
  • MyNCBI (allows you save searches and data important to you)
  • Swiss-Shop at Expasy (BLAST sequence and keyword searches against SwissProt updates)
  • Amedeo (free alert service that searches the MEDLINE database weekly)
  • LeadDiscovery's DailyUpdates (breaking publications from PubMed judged to be of importance to the drug development community)

EMBnet logo
Development of PubCrawler was supported by EMBnet

Last modified at $Date: 2009/04/20 14:22:55 $
For question or remarks, please e-mail pubcrawlerREMOVECAPShelp@gmail.com.