Statistical Analysis of Protein Sequences.
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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 Sequence
Sequence Input Form
One or more sequences to be analysed can be entered directly into this form. Sequences can be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted.
Sequence File Upload
A file containing one or more valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) can be uploaded and used as input for the translation. 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.
Step 2 - Set Parameters
|The output will come with documentation that annotates each part of the report; this option should be set when SAPS is used for the first time as it provides helpful explanations with respect to the statistics being used and the layout of the output.||documented|
|Output limited to analysis of the charge distribution and of high scoring segments.||terse|
|More detailed output.||verbose|
Default value is: default
Uses the specified species table for quantile comparisons
|Gallus gallus (Chicken)||CHICK|
|Drosophila melanogaster (Fruit fly)||DROME|
|Escherichia coli (strain K12)||ECOLI|
|Homo sapiens (Human)||HUMAN|
|Mus musculus (Mouse)||MOUSE|
|Rattus norvegicus (Rat)||RAT|
|Xenopus laevis (African clawed frog)||XENLA|
|Saccharomyces cerevisiae (Baker's yeast)||YEAST|
|Random sample of proteins from Swiss-Prot, Release 23.0||swp23s|
Default value is: Random sample of proteins from Swiss-Prot, Release 23.0 [swp23s]
By default, SAPS treats only lysine (K) and arginine (R) as positively charged residues. Alternatively, Histidine (H) can also be treated as positively charged in all parts of the program involving the charge alphabet.
|Lys, Arg, His||lys-arg-his|
Default value is: Lys, Arg [lys-arg]
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 email@example.com 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).