ArrayPitope performs residue-level epitope mapping of antigens of interests based on peptide microarray data.
This tool has been designed with peptide microarray studies in mind that aims to characterize linear antibody epitopes using an exhaustive amino acid substitution analysis of peptides originating from target antigens.
Submission is divided into four steps
Upload array file
Upload or paste antigen sequences
(optional) Tweak additional parameters
Submit the job
1. Array file
The array file should be a comma or tab separated file containing
rows of peptide sequences and corresponding signal value. The rows may
also contain a sector name (e.g. array well "A01") or a wavelength value
(e.g. "552" or "IgE").
A header row should state clearly what the different columns contain. The following column terminologies can be used (capitalization doesn't matter):
Column type Synonyms accepted
Signal Required signal, sig, raw, pm, intensity
Sequence Required seq, sequence, peptide, oligomer, coresequence, probe_sequence
Sector sec, sector, well
Wavelength wavelength, nm
The file should be gzip compressed and should not exceed 50 Mb in size. For an example of array file, see the Sample data section.
Note: Any peptide sequences not derived (including single amino acid substitution) from the supporting antigen sequence file will not be processed.
2. Antigen sequences
These sequences are used for guiding the mapping of array peptides back to its original antigen sequence and to identify substituted peptides.
The sequences must be in
The sequences can be pasted into the input field in FASTA format instead of uploading a file.
Note: Antigen sequences with no derived array peptides will not be reported in the output.
3. Additional options
The following default algorithm parameters can be customized by the user:
Choose sectors to include
In case that the processing of all array wells in the uploaded data is undesired,
specify which wells should be processed by entering the names of the wells in a
comma separated list, e.g.
A01,A03,A04. In case of numeric wells (0-99) you can also specify a range,
Choose how to handle array layout
If the microarray is designed with physically separated sectors (wells), tick
Handle sectors individually checkbox. This will ensure that
peptides in one well is not normalized against deriving peptides in another
well, subjected to a different treatment.
Choose significance threshold
The statistical inference in the algorithm uses a default significance threshold of 0.0001,
which means that there is less than 0.01% chance that the null hypothesis is rejected incorrectly
(false positive). Other thresholds are available from the dropdown menu under
Significance Threshold Alpha.
Specify peptide length manually
The algorithm cannot process multiple peptide lengths. In case of multiple peptide
lengths in the array data, you can specify the peptide length that you wish to have
processed. By default the algorithm uses the data to find the most frequent length.
4. Submit the job
Click on the
"Submit" button. The status of your job (either 'queued'
or 'running') will be displayed and constantly updated until it terminates and
the server output appears in the browser window.i
At any time during the wait you may enter your e-mail address and simply leave
the window. Your job will continue; you will be notified by e-mail when it has
terminated. The e-mail message will contain the URL under which the results are
stored; they will remain on the server for 24 hours for you to collect them.