Importnat Steps - Following steps should be followed while using RNAint server
Job Title [optional]: This is an optional field. job title name may have letters and number with the "-" or "_". All other character are non-permissible. The job title is only used for your information. It may be a problem with #,$,@ or an empty space within the title of the job, which is not allowed for reasons of security.
E-mail [optional]: Sometimes sequence processing takes more time due to more number of input sequences, few stringent options selected which requires more computational time. Thus, 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 user automatically. After receiving the email, please click on the web-link in the email and access your results page. The web-link of result page will be automatically deleted after one week.
Input sequence: RNAint requires protein sequence in standard FASTA format (User can submit/upload multiple protein sequences). There are two ways of sequence submission. Either directly paste into the text-box or upload the text file using 'BROWSE' option. Before uploading please ensure that the sequence must be in FASTA format and single-letter code of amino acid representation.
Prediction Model Options: RNAint provides five different prediction models for the mono-, di-, tri, tetra- and penta residues predictions. All the SVM models have been developed specifically for the length of RNA-interacting site (RIS). E.g. if user wants to predict RNA-interacting tri-residues than RNAint will predict RIS of only tri-residue or more than 3 residues, it will not predict mono or di-residues.
SVM Threshold Options: All prediction modules have been developed using Support Vector Machine (SVM). Depending upon the threshold value which user choices, SVM will classify the unknown resideus of protein sequence into interacting or non-interacting residues. The default threshold is 0.0. If user want less sensitivity but more specificity, then higher threshold value should be specified, but if opposite is anticipated then lower threshold value should be choosen. So, the expected outcome will depends on the trade-off between sensitivity and specificity.
Probability Score: The probability score is a measure of correct prediction. Where SVM score of more than 1.5 and less than -1.5 fixed with 1.5 and -1.5 respectively. RNAint predicts interaction probability score for each residue of given protein sequence. The probability score varies from 0-9 for each residue of protein sequence. The probability scores ranges between 0-4 and 5-9 predicted as non-interacting and interacting residues respectively (at 0.0 threshold).
A sample of Job Submission Form given below
During job processing...RNAint shows this message (below)
Prediction result - an example of RNA interacting residue prediction (below)
