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, 32 (Web Server issue), W16-9

PubCrawler: Keeping Up Comfortably With PubMed and GenBank


PubCrawler: Keeping Up Comfortably With PubMed and GenBank

Karsten Hokamp et al. Nucleic Acids Res.


The free PubCrawler web service ( has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. A new output format and more flexibility for the email formatting help PubCrawler cope with increasing challenges arising from browser incompatibilities and mail filters, therefore making it suitable for a wide range of users.


Figure 1
Figure 1
A sample output from a PubCrawler results page. An index at the top provides a quick overview of how many new results were retrieved for each query. Aliases can be used to provide descriptive handles for them. Numbers are reported for the total amount of hits and for the previously unseen items that are filtered out for presentation. Older hits are accessible through links up to an adjustable age limit. Multiple queries can be combined under the same alias. Hyperlinks help navigating through the page to get easily from one section to the next. For each article or sequence a checkbox is provided. Using these allows narrowing down the list of interesting items, which can then be retrieved with the click of a button in a format of choice from the NCBI site.
Figure 2
Figure 2
Overview of PubCrawler accounts. The graph presents the total number of new registrations (sum of grey and black bars) as well as the total number of active accounts (black bars), which are those with one or more queries configured and a working email address. For each year's end a horizontal line indicates the number of active accounts and the differences per year are expressed in numbers.

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