DbClustal

Introduction

DbClustal takes the results from a protein BLAST search that you provide and creates a multiple sequence alignment using ClustalW2. Both the BLAST tool output and your original query sequence are needed as inputs.

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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 - Sequence

Sequence Input Window

Query protein sequence used to perform the BLAST search which produced the BLAST report used as input. A free text (raw) sequence is simply a block of characters representing a DNA/RNA or Protein sequence. The sequence can be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format. 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.

Sequence File Upload

Query protein sequence used to perform the BLAST search which produced the BLAST report used as input. A file containing valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot) can be used as input for the sequence similarity search. Word processors 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 input.

Step 2 - Upload BLAST report

BLAST Report Input Window

The BLAST report produced by a blastp search using the input query sequence against a protein database. Works best with NCBI BLAST results from the EBI server. There is a size limit of 2MB on the BLAST report.

BLAST Report Upload

The BLAST report produced by a blastp search using the input query sequence against a protein database. Works best with NCBI BLAST results from the EBI server. There is a file size limit of 2MB on the BLAST report.

Step 3 - Enter Your Parameters

Output Alignment Format

Format for generated multiple sequence alignment.

Order Description Abbreviation
ClustalW ClustalW alignment format default
GCG MSF GCG Multiple Sequence File (MSF) alignment format gcg
PHYLIP PHYLIP interleaved alignment format phylip
NEXUS NEXUS alignment format nexus
NBRF/PIR PIR sequence format pir
GDE GDE sequence format gde
FASTA FASTA sequence format fasta

Default value is: ClustalW [default]

ID List Upload

A file containing a list of hit identifiers from the input BLAST report to include in the multiple sequence alignment. If not set all the hits in the BLAST report will appear in the final alignment.

Step 4 - 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

DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.
(2000 Aug 01) Nucleic acids research 28 (15) :2919-26
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 Apr 06) Nucleic acids research
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