Services
NetCorona - 1.0
Coronavirus 3C-like proteinase cleavage sites in proteins
NetCorona predicts coronavirus 3C-like proteinase (or protease) cleavage sites using artificial neural networks on amino acid sequences. Every potential site is scored and a list is compiled in addition to a graphical representation. Refer to publication for more detailed information and performance values.
Submission
Restrictions:
At most 10 sequences and 50,000 amino acids per submission;
each sequence not more than 10,000 amino acids.
Confidentiality:
The sequences are kept confidential and will be deleted
after processing.
CITATIONS
For publication of results, please cite:
Coronavirus 3CL-pro proteinase cleavage sites: Possible
relevance to SARS virus pathology
L. Kiemer, O. Lund, S. Brunak, and N. Blom
BMC Bioinformatics 2004, 5:72
Download the PDF
Instructions
1. Specify the input sequences
All the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:Please note that the sequences containing other symbols e.g. X (unknown) will be discarded before processing. The sequences can be input in the following two ways:
-
Paste a single sequence (just the amino acids) or a number of sequences in
FASTA
format into the upper window of the main server page.
- FASTA file on your local disk, either by typing the file name into the lower window or by browsing the disk.
Both ways can be employed at the same time: all the specified sequences will
be processed. However, there may be not more than 10 sequences
in total in one submission. Sequences exceeding 10000 amino acids will be ignored.
2. Customize your run
The button "Generate graphics" is used to disable the graphics generated by default. If disabled only the text output is shown.3. Submit the job
Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.
Output format
DESCRIPTION
The first part is an output in HOW format which contains on the first line the number of residues and the sequence name. Then follows the amino acid sequence and below is a representation of each amino acid with the corresponding prediction ('C' for cleavage site and '.' for nothing).
The second part is a listing of the examined residues (glutamines), their score, and in case the score exceeds the 0.5 threshold the amino acids around the cleavage site.
The third part is a graphical representation of the table in the second part of the output.
Multiple sequences are separated with '//'.
EXAMPLE OUTPUT
703 AT6B_HUMAN MAELMLLSEIADPTRFFTDNLLSPEDWGLQNSTLYSGLDEVAEEQTQLFRCPEQDVPFDGSSLDVGMDVSPSEPPWELLP 80 IFPDLQVKSEPSSPCSSSSLSSESSRLSTEPSSEALGVGEVLHVKTESLAPPLCLLGDDPTSSFETVQINVIPTSDDSSD 160 VQTKIEPVSPCSSVNSEASLLSADSSSQAFIGEEVLEVKTESLSPSGCLLWDVPAPSLGAVQISMGPSLDGSSGKALPTR 240 KPPLQPKPVVLTTVPMPSRAVPPSTTVLLQSLVQPPPVSPVVLIQGAIRVQPEGPAPSLPRPERKSIVPAPMPGNSCPPE 320 VDAKLLKRQQRMIKNRESACQSRRKKKEYLQGLEARLQAVLADNQQLRRENAALRRRLEALLAENSELKLGSGNRKVVCI 400 MVFLLFIAFNFGPVSISEPPSAPISPRMNKGEPQPRRHLLGFSEQEPVQGVEPLQGSSQGPKEPQPSPTDQPSFSNLTAF 480 PGGAKELLLRDLDQLFLSSDCRHFNRTESLRLADELSGWVQRHQRGRRKIPQRAQERQKSQPRKKSPPVKAVPIQPPGPP 560 ERDSVGQLQLYRHPDRSQPAFLDAIDRREDTFYVVSFRRDHLLLPAISHNKTSRPKMSLVMPAMAPNETLSGRGAPGDYE 640 EMMQIECEVMDTRVIHIKTSTVPPSLRKQPSPTPGNATGGPLPVSAASQAHQASHQPLYLNHP ................................................................................ 80 ................................................................................ 160 ................................................................................ 240 ................................................................................ 320 .....................................C.......................................... 400 ................................................................................ 480 ................................................................................ 560 ................................................................................ 640 ............................................................... Pos Score Cleavage ___________________________ 30 0.251 none 45 0.067 none 47 0.063 none 54 0.067 none 86 0.235 none 148 0.069 none 162 0.153 none 188 0.169 none 222 0.063 none 245 0.462 none 270 0.393 none 274 0.075 none 285 0.108 none 291 0.102 none 329 0.065 none 330 0.066 none 341 0.281 none 351 0.333 none 358 0.916 EARLQ^AVLAD 365 0.067 none 366 0.062 none 434 0.066 none 445 0.061 none 449 0.100 none 455 0.196 none 459 0.064 none 465 0.064 none 471 0.125 none 494 0.068 none 521 0.073 none 524 0.080 none 532 0.071 none 535 0.071 none 538 0.063 none 541 0.082 none 555 0.073 none 567 0.083 none 569 0.085 none 578 0.071 none 644 0.076 none 669 0.072 none 689 0.150 none 692 0.097 none 696 0.079 none ___________________________//
References
Coronavirus 3CL-pro proteinase cleavage sites: Possible relevance to SARS virus pathology
Lars Kiemer, Ole Lund, Søren Brunak, and Nikolaj Blom
BMC Bioinformatics 2004, 5:72
PMID: 15180906
doi: 10.1186/1471-2105-5-72
Abstract
Results: We retrieved sequence data on seven fully
Conclusion: Our prediction method NetCorona predicts