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
format into the window facing Input sequences.
Select a FASTA
file on your local disk after pressing the button saying "Choose file".
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,(...)"..
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".