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).