Epipe instructions

1. Specify the input

Input sequences:This section allows you to input your sequences. The sequences must be in fasta format and in the one-letter amino acid code (not case sensitive). That code allows the following letters:

A C D E F G H I K L M N P Q R S T V W Y

Please note that the sequences containing other symbols e.g. X (unknown) will be discarded before processing. The sequences can be input by one of the following two ways:

• Paste a number of sequences in FASTA format into the window facing Input sequences.

• Select a FASTA file on your local disk after pressing the button saying "Choose file".

Multiple alignment:You need to input more than one sequence for Epipe to evaluate the differences in predicted features between the two sequences. Given that many of these features are position specific, Epipe needs to align the sequences. You can use one of Epipe's several alignment options or you can input sequences already aligned. In the latter case, under "Multiple alignment", you should click "No,(...)". In the former, click "Yes,(...)"..

Alignment method:If Epipe is to align your sequences, you can choose which "Alignment method" to use. The default is T-Coffee, but you can also choose Clustal, Dialign or HMM Align. Depending on the relationship between your sequences (alternative splicing transcripts, homologous sequences, sequences having only individual variation, etc.) you might prefer particular methods or particular alignment parameters.Give advice on particular methods and datasets in more detail here

Alignment parameters:Still needs to be done

Gene sequence of unspliced transcript:Option not yet implemented
When your dataset consists of sequences resulting from alternative splicing, the safest way to ensure an optimal alignment is to provide the gene sequence that originated all the protein sequences. If this is the case, you can submit your gene sequence (in fasta format, nucleotide sequence) by pressing "Choose file".

2. Select features for analysis

Epipe can compare your sequences across many different features. You can choose which ones to use by checking the box next to its name. The features are grouped by categories, derived from the Biosapiens ontology. By clicking in the category names, the features under that category expand or disappear.
Each feature occupies a line in your screen. It starts by the checkbox to select it, and the you will find the name of the web server that predicts that feature, with a link to its website. Next to it you will find the feature name, and on the right the corresponding ontology. Some ontologies have subdivision, who can be visualized by placing your mouse cursor over the ontology. Clicking the ontologies will give you more information about them. There is also the possibility of selecting or deselecting all features.

3. 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.

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.