EMBL-EBI to be HTTPS by default from 1st December

On the 1st December the majority of services hosted on www.ebi.ac.uk will be served over HTTPS by default. Services that are becoming HTTPS by default will automatically redirect users accessing the site on insecure HTTP URLs to secure HTTPS URLs.
Users of EMBL-EBI services may wish to update links, bookmarks or API clients to use the HTTPS URLs.


Service Retirement

Wise2DBA and Promoterwise are scheduled for retirement on 15th April 2018. Alternatives can be found at Exonerate, BWA or BLAT. If you have any concerns, please contact us via support.

PROSITE Scan

Introduction

PS_SCAN - compare a protein sequence against the signatures in PROSITE.

Official Website
Download Software

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. 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 valid sequence in FASTA or UniProtKB/Swiss-Prot format can be used as input. 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 alignment options

Format

Output format

Format Name Abbreviation
Scan scan
Fasta fasta
PSA psa
MSA msa
GFF gff
PFF pff
Sequence sequence
Match List matchlist

Default value is: Scan [scan]

Database

Choose database to scan.

Database Name Abbreviation
PROSITE prosite
HAMAP profile hamap

Default value is: PROSITE [prosite]

Scan Control

Choose to scan Patterns and/or Profiles.

Name Abbreviation
Patterns and Profiles both
Patterns only patterns
Profiles only profiles

Default value is: Patterns and Profiles [both]

Common Match

Choose to report common matches or not.

Default value is: No [false]

Overlapping Match

Choose to report overlapping matches or not.

Default value is: No [false]

Profile Threshold

Cut-off level for profiles.

Default value is: 0

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

ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins.
(2006 July 01) Nucleic acids research 34 (Web Server issue) :W362-5
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 July 01) Nucleic acids research 43 (W1) :W580-4
Analysis Tool Web Services from the EMBL-EBI.
(2013 July) Nucleic acids research 41 (Web Server issue) :W597-600