This section outlines the ways in which the Pfam website handles information about users. This should not be read as a legal document, but as a description of how we handle information that could be considered sensitive. If you have any concerns about the way that information is used in the website, please contact us at and we will be more than happy to discuss your concerns.

Although we make every possible effort to keep this site and the data that it manipulates safe and secure, we make no claim to be able to protect sensitive or privileged information. If you are at all concerned about sensitive information being released, please do not use the site and consider installing the Pfam database and/or this website locally.

Google analytics

We use Google analytics (GA), to track the usage of this website. GA uses a single-pixel “web bug” image, which is served from every page, a javascript script that collects information about each request, and cookies that maintain information about your usage of the site between visits. You can read more about how GA works on the GA website, which includes a detailed description of how traffic is tracked and analysed.

We use the information generated by GA purely for audit and accounting purposes, and to help us assess the usefulness and popularity of different features of the site. It does not provide the ability to track individual users’ usage of the site. However, GA does provides a high-level overview of the traffic that passes through the site, including such information as the approximate geographical location of users, how often and for how long they visited the site, etc.

We understand that this level of tracking may be worrying to some of our users. If you have any concerns about our use of Google analytics, please feel free to contact us.


All web servers maintain fairly detailed logs of their activity. This includes keeping a record of every request that they serve, usually along with the IP address of the client that made the request. This is true of the web servers that host the Pfam websites.

Although our servers do collect information about your IP address during the normal process of serving the Pfam website, we do not use this information explicitly. The Pfam group uses server logs only to help with development and debugging of the site.


The sequence search feature of the site allows you to upload a protein or DNA sequence to be searched against our library of HMMs. The sequence that you upload is stored in a database and is retrieved by a set of scripts that actually perform the search. Although we do not have any information that could be used to link that sequence to you personally, you should be aware that the sequence itself is accessible to systems administrators and other users who maintain the Pfam site.

The batch search function allows you to submit larger searches, the results of which are emailed to you. Obviously, this requires you to provide identifiable information, namely an email address. However, beyond the routine backups of our databases, we do not store any information about email addresses and sequences in the longer term and we make no attempt to keep track of the searches that a particular user may be performing.

Information from other types of search, such as a keyword search, is held only in the web server logs but, as described above, no attempt is made to interpret these logs except as part of development or debugging of the site.


We use the following cookies to maintain some information about you between your visits to the site. The information that is stored cannot be used to identify you personally and cannot be used to track your usage of the site.

Cookies used in the Pfam site

Cookie name




Timestamp when annotation submission form was loaded in browser



Keep track of whether blog posts have been hidden in home page


In addition to these Pfam-specific cookies, GA uses a series of cookies. You can read more about these in the GA documentation , or in EMBL-EBI’s cookie policy.

If you are at all concerned about the use of cookies in the Pfam site, you are free to block all cookies from this site and you should not experience any problems. You may see some unintended behaviour, such as being notified of all new features every time you visit the index page, but the core functionality of the site should be unaffected.

Third-party javascript libraries

This site makes heavy use of javascript and relies on javascript libraries that are developed by various groups and companies. In order to improve the performance of the Pfam website, we no longer serve these files ourselves, but rely on files that are hosted on third-party web-servers. In particular, we use various files that are provided by the AJAX libraries APIs, hosted by google code, and components of the Yahoo! User Interface Library (YUI), hosted by Yahoo!.

As these services are provided by commercial sites, it’s likely that their usage will be carefully monitored by the companies that provide them. Although the Pfam site does not pass any information about you to these third-party sites, the sites themselves may use cookies to track your usage of the files that they serve. If you are concerned about the privacy implications of this monitoring, you may want to block cookies from the third-party hosting sites.