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Job Title:The user can give job title or sequence name which will become 'subject' in the Email.
E-mail Address:As sequence processing sometimes takes more time due to more number of input sequences,few stringent options selected which requires more computational time, it is advisable to give Email ID to run the process instead of waiting for a long time to publish result at the terminal itself.User can then stop the process and submit new job.All the job result will be mailed to him.
Protein Sequence:Protein sequence(s) can be pasted directly in the box provided only in fasta format. Input can also be given from the file by using 'browse' button. Ideally the input should only be from one source either through box or file but not both.The server also has the capability to ignore all the non-standard characters such as *%!@$% etc present in the input sequence.
Intein Prediction:Models are being created by exploiting different features or patterns of the input sequence using Support Vector Machine (SVM). Two models for intein prediction has been provided. Dipeptide (default) model performs better than amino acid composition model.
Thresold can be selected from the drop down menu.SVM will classify the input sequence(s) as positive or negative based on the thresold selected by the user.If less sensitivity but more specificity is required, then higher threshold value should be specified, but if opposite is needed then lower threshold value is better. Therefore, the expected outcome is a trade-off between sensitivity and specificity. Default thresold is -0.6.
Intein's Splice site Prediction:Three separate models are available for N terminal, C terminal and both N/C splice site prediction.Default is both N/C model and thresold for splice site prediction is -0.9.
If you still have any doubt or some suggestion then feel free to contact us.
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