User guide A tutorial for the antimicrobial sequence scanning system
Introduction
The AMPA algorithm uses an antimicrobial propensity scale to generate an antimicrobial profile by means of a sliding window system.
The propensity scale has been derived using high-throughput screening results from the AMP bactenecin 2A, a 12-residue peptide for which antimicrobial IC50 values for all amino acid replacements at each position have been determined.
From the IC50 for each substitution, an antimicrobial index for individual residues can be calculated (Table 1) that provides a fair assessment of the tendency of such amino acid to be found within an AMP sequence.
As low IC50 values correspond to high activity, amino acids with a low antimicrobial index are the most favored to be part of an AMP.
| Residue | Arg | Lys | Cys | Trp | Tyr | Ile | Val |
| PV | 0.106 | 0.111 | 0.165 | 0.172 | 0.185 | 0.198 | 0.200 |
| Residue | His | Asn | Thr | Phe | Leu | Gln | Gly |
| PV | 0.202 | 0.240 | 0.242 | 0.246 | 0.246 | 0.248 | 0.265 |
| Residue | Met | Ser | Ala | Pro | Glu | Asp | |
| PV | 0.265 | 0.281 | 0.307 | 0.327 | 0.449 | 0.479 |
Analyzing your sequence
Step 1. Entering your sequence
Enter your sequence in the protein box in the FASTA format. An example (consisting on 3 antimicrobial and 3 non-antimicrobial sequences) is provided in the web only by clicking in the sample link. Alternatively, you can upload the sequence as a text file using the uploading tool provided in the webpage
Step 2. Selecting the scanning parameters
The AMPA screening system has been optimized to work with the default window size and threshold value provided. However, experienced users may want to adjust these parameters for specific purposes such as analyzing very large or short proteins or analyze sequences using very stringent criteria. If this is the case you can vary the window size or the threshold value only by modifying the default values in the window or threshold boxes respectively.
If you want to detect a large domain in a huge protein (>500-1000 amino acid residues) you can use a window size from 9 to 19 residues. We do not recommend larger window sizes, as the profile can be difficult to analyze.
If your sequence is very short (< 25 amino acid residues) you can adjust the window size to 5 only if the predicted results obtained with the default parameters are not satisfactory.
Threshold values are only used to determine the length of antimicrobial stretches and do not influence the antimicrobial profile. If your sequence has more than one antimicrobial region and you want to find the most prone antimicrobial stretch you can lower the threshold below the default value. We do not recommend adjusting this parameter and definitely not lowering the threshold value.
Step 3. Providing your email address
You may want to provide the server with your email address. If you fill this box your results will be notified you by email.
The output
After submitting your job the sequence will be processed and the output webpage will be displayed.
In the output page you will find the information on the antimicrobial stretches of your protein: the number and location of the antimicrobial, the mean antimicrobial index of both the protein and the predicted stretches as well as a misclassification probability value, namely the probability that the predicted stretch is found by chance in a non-antimicrobial protein.
You will find also an interactive antimicrobial profile of your sequence together with a table for the average antimicrobial index for each amino acid.
Cite
If you found this server useful, please cite our works:
Contacts
For any question or suggestion on the AMPA server, please contact us at:
marc (dot) torrent (at) upf (dot) edu
paolo (dot) ditommaso (at) crg (dot) es
AMPA is hosted by the 