Table of Contents
The first step in entering data into BayesFold is to paste in the alignment and its associated information. The input screen is shown below:
To input your data,
Enter a name for the alignment. If left blank, this will be filled in with a default name based on current date and time.
Enter the folding temperature. This should be the temperature at which the structures for this alignment are expected to exist. The default value is 37 degrees Celsius.
Enter the primers if not included in sequences. If primers are not included in the alignment you will paste in, then they should be entered here. Otherwise, these fields should be left blank.
Enter label and sequence information. This information can be entered in one of two formats:
Single line: Each sequence is on a single line. If labels exist, each label and sequence pair is on a single line separated by space(s). Labels that themselves contain spaces must be enclosed in either single or double quotes; in this case, the type of quotes used to enclose the label must not appear within the label itself.
FASTA: Lines containing labels begin with a ">" character. All other lines are assumed to hold sequence data.
In both cases, each sequence may contain only the letters A, G, C, U, and T to represent nucleotides, and periods, hyphens, underscores, and tildes to represent gaps. Letters may be entered in either upper or lower case. T's will be automatically converted to U's.
NOTE:
Sequences submitted over the web are limited to a maximum length of 150. This restriction can be removed by installing BayesFold on a local machine.
Click the "Validate" button. This will check the data you entered for any format problems. If any are found, the appropriate message(s) will be displayed in red under the relevant text box. In this case, correct the errors and click Validate again. When the entered data passes validation, the "Continue" button will become active.
Click the "Continue" button to move to the next input step. In that step, you will have a chance to check the data you have entered.
If you want to start over, click the Clear button to discard all the data you have entered and begin again.
Because BayesFold performs best on sequences without runs of gaps or degenerate nucleotides, you will receive a warning if any of the sequences in your alignment contain runs of three or more such positions. This warning provides a reminder that you may get better results by folding sequences that are more similar and/or better characterized, but does not prevent the folding of degenerate or gapped sequences. To continue with folding the original sequences, press the OK button on the warning dialogue; to return to the input screen and alter the sequences, press Cancel.