PromoterWise

Introduction

PromoterWise compares two DNA sequences allowing for inversions and translocations, ideal for promoters.

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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

First Input Sequence

The first DNA sequence to be aligned can be entered directly into the form. The sequence must be in a recognised format eg. GCG, FASTA, EMBL, GenBank. Partially formatted sequences are 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. There is a limit of 1MB for the sequence entry.

First Sequence File Upload

A file containing valid a DNA sequence in any format (GCG, FASTA, EMBL, GenBank) can be used as input for the alignment. Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters. There is a limit of 1MB for the sequence entry.

Second Input Sequence

The second DNA sequence to be aligned can be entered directly into the form. The sequence must be in a recognised format eg. GCG, FASTA, EMBL, GenBank. Partially formatted sequences are 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. There is a limit of 1MB for the sequence entry.

Second Sequence File Upload

A file containing valid a DNA sequence in any format (GCG, FASTA, EMBL, GenBank) can be used as input for the alignment. Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters. There is a limit of 1MB for the sequence entry.

Step 2 - Set alignment options

Hit Output Format

Hit list output format

Order Description Abbreviation
pseudoblast pseudoblast
xml xml
tab tab

Default value is: pseudoblast

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

The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates.
(2005) Genome biology 6 (12) :R104
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600