Table 2 List of all the programs run in ReVac and their predicted features, with the scoring scheme for each programs output. Additional scoring descriptions based on outputs from multiple programs are listed at the bottom
Module (Reference) | Gene property | Evidence | Output | Scoring weight (points) | Example Protein (M. catarrhalis NAO366_1291) | Example Feature | Example Weight | Example Cumulative Score |
|---|---|---|---|---|---|---|---|---|
PSORTb* [13] | Surface exposure^ | Sub-cellular localization | Surface localization prediction | + 1 if surface exposed | 9.52|OuterMembrane | Positive surface exposure | 1 | 1 |
−1 if cytoplasmic | ||||||||
LipoP [14] | Surface exposure^ | Lipoprotein motif | Presence or absence of a motif | 1 or 0 | SpI|18.809 | Positive for lipoprotein motif | 1 | 2 |
TMHMM [15] | Surface exposure^ | Transmembrane spans | Number of helices | If surface exposed < 2: + 0.5 | 1 | Presence of 1 TMH | 0.5 | 2.5 |
02:00.0 | ||||||||
3: −0.2 | ||||||||
≥4: −2 | ||||||||
If cytoplasmic | ||||||||
−2 | ||||||||
SignalP [16] | Surface exposure^ | Signal peptide | Signal peptide | + 1 for presence | MNKTSTQLGLLAVSVSLIMASLPAHA | Signal peptide present | 1 | 3.5 |
SPAAN [17] | Surface exposure^ | Adhesin protein | Adhesin protein score | + 0.5 if above cutoff score (default 0.75) | 0.907057 | Predicted Adhesin | 0.5 | 4 |
Surface HMMs [18]a | Surface exposure Function | HMM for motif or function | HMM title and score | 0.5 | None | No HMM alignment | 0 | 4 |
Antigenic [19] | Antigenicity | Antigenic epitopes | Peptides, scores, protein coverage | 0.5 | QLGLLAVSVSLIMASLPAHAVYLDR|1.193|10(169)|41.73 | Predicted antigenic region. | 0.5 | 4.9173 |
+ 0–1 proportional to coverage | 41.73% of the protein is antigenic | 0.4173 | ||||||
Bcell Pred [20] | Antigenicity | B cell epitopes, 6 prediction methods combined | Number of peptides, protein coverage | + 0–1 proportional to coverage | 6(59)|14|14.57 | Predicited B-cell Epitopes | 0.1457 | 5.09809 |
+ 0–1 proportional to total number of peptides of a given length per protein | 14.57% predicted in 14 peptides of 7AA | 14/(405–7 + 1) = 0.03509 | ||||||
MHC class I [20] | Antigenicity | MHC-I epitopes | Number of peptides, protein coverage | + 0–1 proportional to coverage if 80–90% | 6(378)|124|73|93.33 | Predicted MHC binding | 6.41039 | |
+ 0–1 proportional to total number of peptides of a given length per protein | 93.33% predicted in 124 peptides of 9AA | 124/(405–9 + 1) = 0.3123 | ||||||
+ 1 if coverage is > = 90% | 1 | |||||||
NetCTLpan [20] | Antigenicity | MHC-I epitopes | Number of peptides, protein coverage | + 0–1 proportional to coverage if 80–90% | 12(334)|70|12|82.47 | Predicted MHC binding | 0.8247 | 7.41139 |
+ 0–1 proportional to total number of peptides of a given length per protein | 82.47% predicted in 70 peptides | 70/(405–9 + 1) = 0.1763 | ||||||
+ 1 if coverage is > = 90% | ||||||||
Immunogenicity (MHC-I) [20] | Antigenicity | MHC-I epitopes immunogenicity | Number of peptides, protein coverage | + 0–1 proportional to coverage | 7(76)|14|36|18.77 | Predicted immunogenic region | 0.1877 | 8.63435 |
+ 0–1 proportional to total number of peptides of a given length per protein | 14 peptides of 9AA | 14/(405–9 + 1) = 0.035264 | ||||||
+ 1 if coverage is > = 10% | 1 | |||||||
MHC class II [20] | Antigenicity | MHC-II epitopes | Number of peptides, protein coverage | + 0–1 proportional to coverage if 80–90% | 2(404)|315|61|99.75 | Predicted MHC-II binding | 10.43995 | |
+ 0–1 proportional to total number of peptides of a given length per protein | 99.75% predicted in 315 peptides of 15AA | 315/(405–15 + 1) = 0.8056 | ||||||
+ 1 if coverage is > = 90% | 1 | |||||||
BLAT (IEDBb database*) [20] | Antigenicity | Similarity to curated epitopes from IEDB | Protein coverage | + 0–1 proportional to coverage | None | No hits to epitope database | 0 | 10.43995 |
+ 1 if coverage is > 70% | ||||||||
Autoimmunity [5] | Autoimmunity | Similarity to human proteins | Protein coverage | + 1 if no autoimmunity | None | No hits to Human | 1 | 11.43995 |
−2 *(0 to1) proportional to coverage | ||||||||
−2 if coverage is > 20% | ||||||||
Autoimmunity Commensals [5] | Autoimmunity | Similarity to user-defined commensal organisms’ proteins | Protein coverage | + 1 if no autoimmunity | 3(39)|9.63 | 9.63% similarity to commensal | (0.0963)x(− 2) = −0.1926 | 11.24735 |
−2 *(0 to1) proportional to coverage | (Negative feature) | |||||||
−2 if coverage is > 20% | ||||||||
SSRd Finder [4] | Variability of expression | Phase variation | Number of simple sequence repeats | + 1 if no SSR | None | No DNA SSR found | 1 | 12.24735 |
−0.5 for each SSR | ||||||||
−0.25 for each SSR in the promoter | ||||||||
−0.5 for each SSR with frameshift potential | ||||||||
−0.01 times the length of the SSR. | ||||||||
SSRd Finder Protein [4] | Variability of expression | Potential conformational shifts | Number of protein tandem repeats | −0.2 for each protein repeat, max penalty of 1. | None | No protein SSR found | 0 | 12.24735 |
IslandPath [21] | Potential for horizontal gene transfer | Genomic Islands | Presence in a GI | −1 for each protein in a GI | None | Not present in a GI | 0.5 | 12.74735 |
+ 0.5 for absence | ||||||||
Jaccard Clusters [22]† | Conservation | Orthologous clusters | Presence in an orthologous cluster | + 1 for each protein in a COG in > = 90% of genomes in atleast one method | j_ortholog_cluster_3254|63 | Present in > 90% of the genomes | ||
−0.25 for each protein in a COG in < 90% of genomes | ||||||||
PanOCT [23]† | Conservation | Orthologous clusters | Presence in an orthologous cluster | + 1 for each protein in a COG in > = 90% of genomes in atleast one method | PanOCT_cluster_108|63 | Present in > 90% of the genomes | ||
−0.25 for each protein in a COG in < 90% of genomes | 1 | 13.74735 | ||||||
OrthoMCL [24]† | Conservation | Orthologous clusters | Presence in an orthologous cluster | + 1 for each protein in a COG in > = 90% of genomes in atleast one method | orthomcl_cluster1407|63 | Present in > 90% of the genomes | ||
−0.25 for each protein in a COG in < 90% of genomes | ||||||||
LS-BSR [25]† | Conservation | Orthologous clusters | Presence in an orthologous cluster | + 1 for each protein in a COG in > = 90% of genomes in atleast one method | 63 | Present in > 90% of the genomes | ||
−0.25 for each protein in a COG in < 90% of genomes | ||||||||
Attributorc | Function | Annotation & GO Terms | Annotation & GO Terms | + 1 for each GO term in our surface exposed GO db | hypothetical_protein_domain_protein | No conclusive GO terms predicted | 0 | 13.74735 |
−1 for each GO term in our non-surface exposed GO db | ||||||||
+ 1 if presence of surface exposure keywords if predicted periplasmic | ||||||||
aHMM: Hidden Markov Model. This component includes a collection of HMMs selected from the Pfam database for motifs associated with surface proteins. | ||||||||
bIEDB: Immune Epitope Database and Analysis Resource | ||||||||
cIn house Perl/Python script | ||||||||
dSSRs: simple sequence repeats | ||||||||
*If any three of PSORTB, LipoP, SignalP and IEDB Database matches are all positive, weight is incremented by 2. | True | 2 | 15.74735 | |||||
^If all surface exposure tools fail a conclusive prediction, weight is decremented by 2 | False | 0 | 15.74735 | |||||
†Each protein is given an additional 0.1 for > 90% presence in each of the clustering algorithms, Jaccard Clusters, PanOCT, OrthoMCL and LS-BSR, and penalized 0.5 for < 90% presence or absence of a cluster for each tool. | True | 0.4 | ReVac Score = 16.14735 | |||||