GARILC accepts PRISM results output as a JSON file. These files can be downloaded from the PRISM results page. For more help on getting PRISM data refer to PRISM's help page. Upload a PRISM result by selecting "Browse" then "Upload".
Along with PRISM results GARLIC also accepts text input of a scaffold and tailorings. See examples below. Abbreviations are located on the Abbreviations tab.
Scaffold: Amino acids and or polyketide substrates (along with polyketide state). Substrates are separated with a space, polyketide states are appended to a polyketide substrate with a '-'. Separate continuous pieces are separated with a '|'.
Tailoring: Modifications to the molecule such as sulfonations and chlorinations.
Single amino acid chain: Ala Gly Ser Leu
Single polyketide chain: Mem-H Mal-- Mem-K Mem-=
PK/NRP hybrid: Glu Phe | Mem-H Mem-H Mem-H | Ala Lys
Tailorings: Cl ST GTr
GARLIC makes several advanced options available to users with specific needs. General users do not need to configure these parameters.
Alignment type: Two algorithms are available, local and global.
Tailoring: Optionally turn off tailoring scoring, this causes GARLIC to only consider the core scaffold.
Maximum number of alignments: Optionally display more or less alignments. The alignments are sorted from highest to lowest score.
Once the search button is clicked, GARLIC will automatically execute its algorithms for scoring the biosynthetic gene clusters from the input file against known compounds.
Abbreviations listed here are used in the results page and can be used for reference. Abbreviations are also used for inputting scaffold and tailoring data. See Help page for how to manually input scaffolds and tailorings with examples.
Amino Epoxi Oxodecanoic Acid: Aeo
Beta Alanine: bAla
Beta MethylPhenylalanine: MePhe
Beta Phenylalanine: bPhe
Beta HydroxyPhenylalanine: OHPhe
Aspartic Acid: Asp
Hydroxyaspartic Acid: OHAsp
Beta Methyl Aspartic Acid: MeAsp
Glutamic Acid: Glu
Beta hydroxy Valine: OHVal
Hydroxy Ornithine: OHOrn
Hydroxy AcetylOrnithine: HAOrn
Butenyl Methyl Threonine: Bmt
Beta Lysine: bLys
Adipic Acid: Aad
Aminobutyric Acid: Abu
Dehydro Aminobutyric Acid: Dhab
Valeric Acid: Vaa
Diaminobutyric Acid: Dab
Pipecolic Acid: Pip
Piperazic acid: Piz
Methyl Buteryl: MBu:
Benzoyl CoA: Bz
Ethyl Malonate: EtM
Isobuteryl CoA: IBu
Methyl Malonate: MeM
Hydroxy Methyl Malonate: OMeMal
Propionyl CoA: Pr
Ketone (Fully oxidized): K
Hydroxyl (Keto reductase): H
Double bond (Dehydratase): =
Single bond (Enol reductase): -
GARLIC is a project of the Nathan Magarvey Lab at McMaster University. We aim to provide bio- and chemoinformatic solutions for genomic natural product discovery.
GARLIC is an automated scoring method comparing biosynthetic clusters to Natural products. Currently GARLIC takes PRISM1 results as input and will compare the clusters to all known compounds. The compounds have been annotated with the GRAPE algorithm. Results are shown as alignments with extra features.
GARLIC is freely available as an online service for the research community. GARLIC and GRAPE implement the Chemistry Development Kit2, and MCS.3
1 Skinnider, M.A., Dejong, C.A., Rees, P.N., Johnson, C.W, Li, H., Webster, A.L.H., Wyatt, M.A., Magarvey, N.A. (2015) Genomes to natural producs PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic Acids Res
2 Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E. and Willighagen, E. (2003) The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. J. Chem. Inf. Comput. Sci., 43, 493-500.
3 Rahman, S.A., Bashton, M., Holliday, G.L., Schrader, R., and Thornton, J.M. (2009) Small Molecule Subgraph Decector (SMSD) toolkit. Cheminformatics.