Introduction
EMBOSS Water uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment of a sequence to one or more other sequences.
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Important Note
- PSA tool algorithms are NOT intended to produce genome synteny maps.
- We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.
How to Access EMBOSS Water
EMBOSS Water can be accessed via
Web Form
Web interface for EMBOSS Water is available at : https://www.ebi.ac.uk/Tools/psa/emboss_water (protein) https://www.ebi.ac.uk/Tools/psa/emboss_water/nucleotide.html (nucleotide)
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
A free text (raw) list of sequences is simply a block of characters representing several DNA/RNA or Protein sequences. A sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format (Protein only). Partially formatted sequences are not accepted. (See example input formats). 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.
First Sequence File Upload
A file containing valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot (Protein only)) can be used as input for the sequence similarity search. (See example input formats). 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.
Second Input Sequence
A free text (raw) list of sequences is simply a block of characters representing several DNA/RNA or Protein sequences. A sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format (Protein only). Partially formatted sequences are not accepted. (See example input formats). 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.
Second Sequence File Upload
A file containing valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot (Protein only)) can be used as input for the sequence similarity search. (See example input formats). 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.
Step 2 - Set alignment options
Matrix
Default substitution scoring matrices.
Additional information Read more about matrices
Gap Open Penalty
Pairwise alignment score for the first residue in a gap.
Default value is: 10
Additional information Read more about gap penalties
Gap Extend Penalty
Pairwise alignment score for each additional residue in a gap.
Default value is: 0.5
Additional information Read more about gap penalties
Output formats
Pairwise sequences format (example output formats).
| Value | Description |
|---|---|
| pair | The sequences have the markup line between them |
| markx0 | This is the standard default output format used by Bill Pearson's suite of FASTA programs |
| markx1 | This is an alternative output format used by Bill Pearson's suite of FASTA programs in which identities are not marked. Instead conservative replacements are denoted by 'x' and non-conservative substitutions by 'X' |
| markx2 | This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the residues in the second sequence are only shown if they are different from the first |
| markx3 | This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the aligned sequences are displayed in FASTA sequence format. These can be used to build a primitive multiple alignment |
| markx10 | This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the aligned sequences are displayed in FASTA sequence format and the sequence length, alignment start and stop information is given in lines starting with a ';' character just after the title line for each sequence. It is intended to be easily parsed by other programs |
| srspair | This is very similar in style to pair format |
| score | This does not display the sequence alignment. It shows only the names of the sequences, the length of the alignment and the score |
| clustal | Clustal alignment format without base/residue numbering |
| fasta | Pearson or FASTA sequence format |
| msf | Multiple Sequence File (MSF) alignment format |
| nexus | NEXUS alignment format |
| phylip | PHYLIP interleaved alignment format |
| selex | SELEX alignment format |
Default value is: pair
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).
Web Services
Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines.
For an introduction on how to run these clients and use them in workflows please see the webinar series.
REST API
The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
| Language | Download | Requirements |
|---|---|---|
| Perl | emboss_water.pl | LWP and XML::Simple |
Python | xmltramp2 |
For an introduction on how to run these clients and use them in workflows please see the 'EMBL-EBI, programmatically: take a REST from manual searches' webinar series.
WADL
The WADL for the EMBOSS water (REST) service: http://www.ebi.ac.uk/Tools/services/rest/emboss_water?wadl
Tool Parameters
Parameters | Command line parameter |
|---|---|
| --matrix | |
| GAP OPEN | --gapopen |
| GAP EXTEND | --gapext |
| OUTPUT FORMAT | --format |
SOAP API
The Simple Object Access Protocol (SOAP) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
WSDL
The WSDL for the EMBOSS water (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/emboss_water?wsdl
Open API Interface
https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=emboss_water
Common Workflow Language
CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl
For details, see CWL Workflows page.
Reference