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

Introduction

EMBOSS polydot generates a dotplot for each of an all-against-all comparison of a set of sequences. The dotplots are rendered on a single diagram. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence searching for exact matches between sequence regions ("words"). The two sequences are the axes of the rectangular dotplot. Wherever there is "similarity" between a word from each sequences a dot is plotted. The wordsize is specified by the user. Optionally, information on the sequence and location of all the exact matching regions may be written to file as a feature file.

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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

Sequences

Two or more aligned sequences are required.  (See example input formats). There is currently a data limit of 1MB.

File Upload

Two or more aligned sequences are required.  (See example input formats). There is currently a data limit of 1MB.

Step 2 - Set alignment options

Word Size

Word size over which to test threshold. 

Default value is: 6

Gap

This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output.

Default value is: 10

Boxit

Displays the overlapping matches (in red) as well as the minimal set of non-overlapping matches.

Default value is: Yes (True)


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

EMBOSS: the European Molecular Biology Open Software Suite.
(2000 June 01) Trends in genetics : TIG 16 (6) :276-277
PMID: 10827456The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 April 06) Nucleic acids research 43 (W1) :W580-4
PMID: 25845596Analysis Tool Web Services from the EMBL-EBI.
(2013 May 13) Nucleic acids research 41 (Web Server issue) :W597-600
PMID: 23671338


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