A fast and accurate multiple sequence alignment algorithm.
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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
Three or more sequences to be aligned can be entered directly into this form. Sequences can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) 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. There is currently a sequence input limit of 2000 sequences and 2MB of data.
Sequence File Upload
A file containing three or more valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be uploaded and used as input for the multiple sequence 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 currently a file upload limit of 2000 sequences and 2MB of data.
Indicates if the sequences to align are protein or nucleotide (DNA/RNA).
Default value is: Protein [protein]
STEP 2 - Set your Parameters
Format for generated multiple sequence alignment.
|Pearson/FASTA||Pearson or FASTA sequence format||fasta|
|ClustalW||ClustalW alignment format without base/residue numbering||clu|
|MACSIM||Macsim XML alignment format||macsim|
Default value is: ClustalW [clu]
The penalty for opening/closing a gap. Half the value will be subtracted from the alignment score when opening, and half when closing a gap.
Default value is: 11.0
Penalty for extending a gap
Default value is: 0.85
Penalty to extend gaps from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences
Default value is: 0.45
A bonus score that is added to each pair of aligned residues
Default value is: 0.0
Step 3 - Submission
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.
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.
If email notification is requested, then a valid Internet email address in the form firstname.lastname@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).