Exploring Pfam

In this section of the tutorial you will be guided over the Pfam website, accessible through the following url: http://pfam.xfam.org/, and how to find different types of data.

In the Home page, you will find quick links to make different types of queries as shown in the figure below, click on the (i) icons for more details.

Figure 3. Pfam home page.

Pfam search

At the top of the page, there is a SEARCH tab, where you can find more options to perform a range of searches available in the left-hand side panel (Figure 4). One of them is the sequence search, i.e. paste your DNA or protein sequence in FASTA format and select a cut-off for your significant matches or use the default settings (Figure 4). You can find more information about this option by clicking in ‘More…‘ above the Sequence search text box.

Another tab allows to perform a Batch search, where you can submit your Multiple sequence alignment (MSA) to search against our models. Additionally, you can also make a Keyword search and a Taxonomy search, selecting the organism/s you are interested in. Finally, the search by domain architecture allows to select which domains you want to include/exclude in your query (Figure 5).

Browse Pfam

Using the BROWSE tab at the top of the web page you can browse Pfam families, clans or proteomes. They are alphabetically ordered (Figure 6).