Services
NetCGlyc - 1.0
C-mannosylation sites in mammalian proteins
The NetCGlyc 1.0 produces neural network predictions of C-mannosylation sites in mammalian proteins.
Submission
Restrictions
At most 100 sequences per submission;
each sequence not less than 15 and not more than 4000 amino acids, no more than 200,000 amino acids in total.
Confidentiality
The sequences are kept confidential and will be deleted
after processing.
CITATIONS
For publication of results, please cite:
NetCGlyc 1.0: Prediction of mammalian C-mannosylation sites.
Karin Julenius
Glycobiology, 17:868-876, 2007.
View the full text
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:
All the other symbols will be converted to X 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.
- Select a 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 100 sequences in one submission. Sequences shorter than 15
or longer than 4000 amino acids will be ignored.
2. Customize your run
By default the output is in GFF; click on 'short' for a simpler output (see the Output format section for descriptions and examples).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
- sequence name
- prediction source ("netCglyc" and version)
- predicted feature (C-mannosylation)
- residue number
- prediction score (a number in 0.0-1.0)
- non-applicable (GFF specific)
- answer: "W" if the score is greater than 0.5, else "." (dot).
The example below shows the NetCGlyc 1.0 output for ADAMTS-like protein 5 precursor (ADAMTSL-5), taken from the UniProt entry ATL5_HUMAN. One of the 12 tryptophan residues in the sequence (#41) is predicted as C-mannosylated, two more (#38 and #44) have scores close to the threshold.
EXAMPLE OUTPUT
##gff-version 2 ##source-version netCglyc-1.0b ##date 2007-03-14 ##Type Protein # seqname source feature start end score +/- ? # ---------------------------------------------------------------------------- Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 21 21 0.269 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 38 38 0.459 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 41 41 0.639 . W Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 44 44 0.484 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 72 72 0.221 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 115 115 0.285 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 207 207 0.228 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 244 244 0.246 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 299 299 0.160 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 317 317 0.203 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 410 410 0.243 . . Q6ZMM2_ATL5_HUMAN netCglyc-1.0b C-manno 454 454 0.227 . . # ----------------------------------------------------------------------------
References
NetCGlyc 1.0: Prediction of mammalian C-mannosylation sites.
Karin Julenius
Glycobiology, 17:868-876, 2007.
Department of Medical Biochemistry and Biophysics, Karolinska
Institutet, SE-171 77 Stockholm, Sweden
Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-106 91 Stockholm, Sweden