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Input form  |  Web services  |  Help & Documentation  |  Bioinformatics Tools FAQ

Introduction

PfamScan is used to search a FASTA sequence against a library of Pfam HMM.

Official Website

Download Software

EMBL-EBI FTP Download

EMBL-EBI HTTP Download

How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
  • In the following steps, the user has the possibility to change the default tool parameters
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Input Sequences

Input Sequence

The input sequence can be entered directly into this form. The sequence can be in FASTA or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. (See example input formats). Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.

Sequence File Upload

A file containing a valid sequence in FASTA or UniProtKB/Swiss-Prot format can be used as input. (See example input formats). Word processor files may yield unpredictable results as hidden/control characters may be present. It is best to save files with the Unix format option to avoid hidden Windows characters.

Step 2 - Set options

Database

The database(s) to search.

NameValue
Pfam-Apfam-a

Default value is: Pfam-A [pfam-a]

Expectation Value

Expectation value cut-off.

Default value is: 10

Active Site Prediction

Predict active site residues for Pfam-A matches.

NameValueDescription
yestrue
nofalse

Default value is: no [false]

Output Format

Example output formats

NameValueDescription
JSONjsonJSON output format.
Plain TexttxtPlain text output format.

Default value is: JSON [json]

Step 3 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).

References

Predicting active site residue annotations in the Pfam database.
(2007 August 09) BMC bioinformatics 8 :298
PMID: 17688688

The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 April 06) Nucleic acids research 43 (W1) :W580-4
PMID: 25845596

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