MoRFchibi 2.0

MoRFchibi 2.0 [1] predicts Molecular Recognition Features (MoRFs) in amino acid sequences.

In contrast to most predictors, including the old MoRFchibi predictors [2][3][4], where scores represent propensities with higher values indicating greater probabilities and thus can only be understood relative to other scores [5], MoRFchibi 2.0 generates actual probability scores normalized for the priors [5]. That is, the scores generated by MC2 are MoRF probabilities, assuming that 50% of residues in the general population are MoRF residues. Consequently, MC2-generated probability scores are interpretable individually, and there is no need to provide an arbitrary cut-off value to convert them into binary predictions. When such a value is needed, we recommend that each user (researcher) use a cut-off value best suited to their tolerance of false positives/negatives. However, some users may prefer a generic cut-off; in this case, we suggest a value of 0.775 and that sections under four residues above this cut-off not be identified as MoRFs.

To process amino acid sequences, enter (paste) sequences in FASTA format into the input box and click 'Submit Job'. When a job is submitted, each sequence is scanned for input errors and then entered into the queue structure and a job record is inserted into the 'Jobs' table for each sequence. Once a sequence is processed, results are made available through the results page.

Live Results Page Sample Output for P04637 (P53)

Each page holds the outcome of processing one query sequence and is saved in the server for 48 hours. Page life can be renewed manually by clicking the renew button    in the results page, or in the 'Saved For' column of the Jobs table.

The link to the results page is available through the [Ready/Not Ready] button in the 'Results' column of the Jobs table.

If you lose the browser session, links to all results pages will also be lost. If you provide an email address, the server will send you a notification email upon job completion with an attached copy of the results file and a link to the results page. Otherwise, we strongly recommend saving links to result pages manually or bookmarked.

The HTML server processes sequences in standard fasta format. MoRFchibi 2.0 server ignores spaces in the input sequences. When the Case Sensitive option is selected (default case), amino acids can only be represented with uppercase letters, and lowercase letters will generate an error. When not selected, the server can process both lower and upper-case letters, and numbers are ignored and removed from the input sequence.

An example sequence is available by clicking 'Input Example'. To clear the input box, click 'Clear'.

The graph output displays the MoRFchibi 2.0 probability scores for the complete sequence.

The Toggle MoRF Bands option displays or hides the binary MoRF/nonMoRF decision. We identified more than three residue sections with MC2 scores greater than a 0.775 cut-off as MoRFs.

The vertical Propensity scale is adjusted automatically to best fit the data, the Toggle Y-Axis Bounds can be used to change the Y-axis bounds to [0-1].

The menu at the top right corner provides printing or downloading of the graph in PNG, JPEG, PDF, or SVG format.

One can select an area using the mouse to zoom in and then reset it using the button in the lower right corner.

Lines 1 to 8: Results header.

Line 9: The sequence FASTA title

Lines 10 to the end of file:

• Column 1: Sequence residue index.
• Column 2: Sequence residue.
• Column 3: MoRFchibi 2.0 propensity score.

If an email address is provided (providing an email address is optional), a notification email will be sent once a job is processed. Notification emails includes an attached copy of the results file and a link to the results page.

Each 'Job' record has the following fields:

1. Id: a unique integer job id.
2. Label: the job label is the FASTA sequence title. Job labels are not unique.
3. Size [residues]: the size of the sequence in residues.
4. Status: one of following five values:
   • <Processing> The sequence is currently been processed.
   • <Position: x> The job is in the server queue at position x.
   • <Pending> The job is in the private user queue.
   • <Completed in Xs> The job has completed in X seconds.
   • <Failed> Error Message.
5. Results: Provides a link to the results page, and button [Graph] to display the graph.
6. Save For: displays the number of hours left in the results page life. A renew button     renews that life to 48 hours.

A two tier queue system with a server queue and user queues is implemented to prevent a single user of dominating the server with a large number of jobs. In this structure, each user can place up to two jobs in the server queue. If a user submits more than two jobs, those extra jobs will be placed temporarily in that user private queue. Once a user's job in the server queue is completed, the job at the top of that user's queue (if exist) will be moved to the tail of the server queue. User queues are located on the server, thus, once the link to the result page is secured, users can safely close the browser.

• [1] Malhis N and Gsponer J. Computational identification of molecular recognition features (MoRFs) in protein sequences with MoRFchibi 2.0. bioRxiv (2025)
• [2] Malhis N, Jacobson M, and Gsponer J. MoRFchibi SYSTEM: Software Tools for the Identification of MoRFs in Protein sequences. Nucleic Acids Research (2016), DOI: 10.1093/nar/gkw409.
• [3] Malhis N, Wong TCE, Nassar R, Gsponer J. Computational Identification of MoRFs in Protein Sequences Using Hierarchical Application of Bayes Rule. PLOS ONE (2015), DOI: 10.1371/journal.pone.0141603.
• [4] Malhis N, and Gsponer J. Computational Identification of MoRFs in Protein Sequences.  Bioinformatics (2015) 31 (11): 1738-1744.
• [5] Malhis N. Probabilistic Annotations of Protein Sequences for Intrinsically Disordered Features.  bioRxiv (2024) DOI: 10.1101/2024.12.18.629275.