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SAPS

Introduction

Statistical Analysis of Protein Sequences.

Official Website
Download Software

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

Output Type

Output type

Description Value
Deafult output. default
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

Species

Uses the specified species table for quantile comparisons

Species Name Abbreviation
Bacillus subtilis BACSU
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]

Positive Residues

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.

Residues Value
Lys, Arg lys-arg
Lys, Arg, His lys-arg-his

Default value is: Lys, Arg [lys-arg]

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).

References

Methods and algorithms for statistical analysis of protein sequences.
(1992 March 15) Proceedings of the National Academy of Sciences of the United States of America 89 (6) :2002-6
The EMBL-EBI bioinformatics web and programmatic tools framework.
(2015 July 01) Nucleic acids research 43 (W1) :W580-4
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 July) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 July) Nucleic acids research 41 (Web Server issue) :W597-600