FROG stands for FingeRprinting Ontology of Genomic variations. FROG fingerprints have been devised to capture genomic variations at various levels. The assigned fingerprints allow us to make large number of genomic variations computationally efficient in terms of memory requirement and faster retrieval. This interface has been designed to explore structure of FROG fingerprints and search mitochondrial variants using combination of fingerprints of various FROG properties. Click FROG User manual to know more about FROG and this framework.

**If you use FROG fingerprints or this framework for your research, please cite us as
Abinaya E, Narang P, Bhardwaj A (2015) FROG - Fingerprinting Genomic Variation Ontology.
PLoS ONE 10(8): e0134693. doi:10.1371/journal.pone.0134693

Some of the major features of FROG are: FROG consists of six major blocks classified into 48 attributes and 278 terms
 
  • 1. Chromosome (13 bits)
    • 1.1. Variation kind (2 bits)
      • 1.1.1. Indel (01)
      • 1.1.2. Insertion (10)
      • 1.1.3. Deletion (11)
      • 1.1.4. Substitution (00)
    • 1.2. Repeats (3 bits)
      • 1.2.1. Mono-nucleotide expansion Microsatellite (000)
      • 1.2.2. Minisatellite (001)
      • 1.2.3. Mobile elements (010)
      • 1.2.4. Tandem repeats binucleotides (011)
      • 1.2.5. Trinucleotide expansion (110)
      • 1.2.6. Tetranucleotide expansion (111)
      • 1.2.7. Interspersed Hexaploidy (101)
      • 1.2.8. No amplification (100)
    • 1.3. Location (1 bit)
      • 1.3.1. Autosomes (0)
      • 1.3.2. Allosomes (1)
    • 1.4. Variation number (4 bits)
      • 1.4.1. Set number (0)
        • 1.4.1.1. Nulliploidy (010)
        • 1.4.1.2. Monoploidy (001)
        • 1.4.1.3. Diploidy (000)
        • 1.4.1.4. Triploidy (011)
        • 1.4.1.5. Tetraploidy (111)
        • 1.4.1.6. Pentaploidy (101)
        • 1.4.1.7. Hexaploidy (110)
        • 1.4.1.8. Polyploidy (100)
      • 1.4.2. Number (1)
        • 1.4.2.1. Nullisomy (111)
        • 1.4.2.2. Monosomy (011)
        • 1.4.2.3. Disomy (000)
        • 1.4.2.4. Iso-Disomy (001)
        • 1.4.2.5. Hetero-Disomy (010)
        • 1.4.2.6. Trisomy (100)
        • 1.4.2.7. Tetrasomy (110)
        • 1.4.2.8. Polysomy (101)
    • 1.5. Structural variation (3 bits)
      • 1.5.1. Complex (1)
        • 1.5.1.1. Uncharacterized (100)
        • 1.5.1.2. Telomere changes (101)
        • 1.5.1.3. Interstetial deletion (110)
        • 1.5.1.4. Isochromosome (111)
      • 1.5.2. Translocation (0)
        • 1.5.2.1. Intra (0)
          • 1.5.2.1.1. Para intra-translocation (0)
          • 1.5.2.1.2. Peri intra-translocation (1)
        • 1.5.2.2. Inter (1)
          • 1.5.2.2.1. Reciprocal inter-translocation (0)
          • 1.5.2.2.2. Robert inter-translocation (1)
  • 2. DNA (15 bits)
    • 2.1. Variation kind (3 bits)
      • 2.1.1. Indel (000)
      • 2.1.2. Insertion (011)
      • 2.1.3. Deletion (001)
      • 2.1.4. Translocation (111)
      • 2.1.5. Inversion (110)
      • 2.1.6. Transition (010)
      • 2.1.7. Transversion (100)
      • 2.1.8. No defined change (101)
    • 2.2. Transition type (2 bits)
      • 2.2.1. A to G purine transition (00)
      • 2.2.2. G to A purine transition (01)
      • 2.2.3. C to T pyrimidine transition (10)
      • 2.2.4. T to C pyrimidine transition (11)
    • 2.3. Transversion type (3 bits)
      • 2.3.1. A to C transversion (100)
      • 2.3.2. A to T transversion (001)
      • 2.3.3. G to C transversion (011)
      • 2.3.4. G to T transversion (010)
      • 2.3.5. C to A transversion (000)
      • 2.3.6. C to G transversion (111)
      • 2.3.7. T to A transversion (101)
      • 2.3.8. T to G transversion (110)
    • 2.4. Epigenetic variations (1 bit)
      • 2.4.1. DNA methylation(1)
      • 2.4.2. DNA remodelling (0 )
    • 2.5. Gene fusion (1 bit)
      • 2.5.1. Gene fusion occured (1)
      • 2.5.2. Gene fusion not occured (0)
    • 2.6. Structural variation (3 bits)
      • 2.6.1. Secondary structure (1)
        • 2.6.1.1. DNA G-quadruplex (00)
        • 2.6.1.2. I motif (01)
        • 2.6.1.3. Triple stranded (11)
        • 2.6.1.4. DNA stem (10)
      • 2.6.2. Level affected (0)
        • 2.6.2.1. Intron (00)
        • 2.6.2.2. Exon (01)
        • 2.6.2.3. Extra DNA (11)
        • 2.6.2.4. Chromatin (10)
    • 2.7. Function Level (2 bits)
      • 2.7.1. DNA replication (00)
      • 2.7.2. DNA repair (01)
      • 2.7.3. Effect on promoter activity- REG function of DNA (10)
      • 2.7.4. Effect on transcription (11)
  • 3. RNA (23 bits)
    • 3.1. Variation kind (3 bits)
      • 3.1.1. Indel (000)
      • 3.1.2. Insertion (011)
      • 3.1.3. Deletion (001)
      • 3.1.4. Translocation (111)
      • 3.1.5. Inversion (110)
      • 3.1.6. Transition (010)
      • 3.1.7. Transversion (100)
      • 3.1.8. No defined change (101)
    • 3.2. Transition type (2 bits)
      • 3.2.1. A to G purine transition (00)
      • 3.2.2. G to A purine transition (01)
      • 3.2.3. C to U pyrimidine transition (10)
      • 3.2.4. U to C pyrimidine transition (11)
    • 3.3. Transversion type (3 bits)
      • 3.3.1. A to C transversion (100)
      • 3.3.2. A to U transversion (001)
      • 3.3.3. G to C transversion (011)
      • 3.3.4. G to U transversion (010)
      • 3.3.5. C to A transversion (000)
      • 3.3.6. C to G transiversion (111)
      • 3.3.7. U to A transversion (101)
      • 3.3.8. U to G transversion (110)
    • 3.4. Splicing (3 bits)
      • 3.4.1. Cis splicing (1)
        • 3.4.1.1. Place (1)
          • 3.4.1.1.1. 3-prime(1)
          • 3.4.1.1.2. 5-prime (0)
        • 3.4.1.2. Type (0)
          • 3.4.1.2.1. Canonical(1)
          • 3.4.1.2.2. Non-canonical (0)
      • 3.4.2. Other kinds(0)
        • 3.4.2.1. Acceptor-new site generation (00)
        • 3.4.2.2. Donor-new site generation (01)
        • 3.4.2.3. No trans splicing (11)
        • 3.4.2.4. Trans Splicing (10)
    • 3.5. Property changes (3 bits)
      • 3.5.1. No effect (000)
      • 3.5.2. Nonsense (110)
      • 3.5.3. Nonstop (101)
      • 3.5.4. RNA abundance (100)
      • 3.5.5. RNA folding (011)
      • 3.5.6. RNA Interaction (010)
      • 3.5.7. RNA stability (001)
      • 3.5.8. Non-GO (111)
    • 3.6. Secondary structure changes (3 bits)
      • 3.6.1. Loop (1)
        • 3.6.1.1. Hairpin (00)
        • 3.6.1.2. Interior Loop,multi loop (01)
        • 3.6.1.3. Multiloop (11)
        • 3.6.1.4. Uncharacterised Loop (10)
      • 3.6.2. Others (0)
        • 3.6.2.1. Bulge (00)
        • 3.6.2.2. No effect on secondary structure (11)
        • 3.6.2.3. Pseudoknots (10)
        • 3.6.2.4. Stem (01)
    • 3.7. Affected Level (3 bits)
      • 3.7.1. Composition (00)
        • 3.7.1.1. Nucleoside (0)
        • 3.7.1.2. Base (1)
      • 3.7.2. Frame changes (11)
        • 3.7.2.1. Outframe (0)
        • 3.7.2.2. Inframe (1)
      • 3.7.3. Coding (01)
        • 3.7.3.1. Exons (0)
        • 3.7.3.2. Introns (1)
      • 3.7.4. Non-genetic (10)
        • 3.7.4.1. decayed-RNA (0)
        • 3.7.4.2. modified RNA (1)
    • 3.8. Mechanism changes (1 bit)
      • 3.8.1. Silent (1)
      • 3.8.2. Non-sense (0)
    • 3.9. Functional changes (2 bits)
      • 3.9.1. Effect on RNA information transfer (00)
      • 3.9.2. Effect on translation (01)
      • 3.9.3. Effect on regulatory activity (10)
      • 3.9.4. Effect on amino acid transfer function of RNA (11)
  • 4. Protein (22 bits)
    • 4.1. Variation kind (2 bits)
      • 4.1.1. Indel (01)
      • 4.1.2. Insertion (10)
      • 4.1.3. Deletion (11)
      • 4.1.4. Substitution (00)
    • 4.2. Accessibility (1 bit)
      • 4.2.1. Buried (1)
      • 4.2.2. Exposed (0)
    • 4.3. Predicted pathogenecity (4 bits)
      • 4.3.1. Sift and Polyphen(1)
        • 4.3.1.1. unknown(p)+tolerated(s) (000)
        • 4.3.1.2. probably Damaging(p)+damaging(s) (001)
        • 4.3.1.3. possibly Damaging(p)+tolerated(s) (010)
        • 4.3.1.4. probably damaging(p)+tolerated(s) (011)
        • 4.3.1.5. unknown(p)+damaging(s) (100)
        • 4.3.1.6. benign(p)+tolerated(s) (101)
        • 4.3.1.7. possibly Damaging(p)+damaging(s) (110)
        • 4.3.1.8. benign(p)+damaged(s) (111)
      • 4.3.2. Either of the above (0)
        • 4.3.2.1. Sift (1)
          • 4.3.2.1.1. Tolerated(01)
          • 4.3.2.1.2. Damaging (10)
          • 4.3.2.1.3. Unknown (00)
          • 4.3.2.1.4. Tolerated low confidence (11)
        • 4.3.2.2. Polyphen (0)
          • 4.3.2.2.1. Possible damaging (00)
          • 4.3.2.2.2. Probably damaging (01)
          • 4.3.2.2.3. Unknown (10)
          • 4.3.2.2.4. Benign (11)
    • 4.4. Protein dynamics (2 bits)
      • 4.4.1. Effect on allosteric site (00)
      • 4.4.2. Effect on induced site (01)
      • 4.4.3. Effect on structure disorder (11)
      • 4.4.4. Effect on structure flexibility (10)
    • 4.5. Property variation (3 bits)
      • 4.5.1. Effect on protein sub cellular localization (000)
      • 4.5.2. Effect on protein accessibility (001)
      • 4.5.3. Effect on protein abundance (010)
      • 4.5.4. Effect on protein electrostatics (011)
      • 4.5.5. Effect on protein degradation (100)
      • 4.5.6. Effect on protein aggregation (101)
      • 4.5.7. Effect on protein activity (110)
      • 4.5.8. Effect on protein precipitation (111)
    • 4.6. Structural variation (5 bits)
      • 4.6.1. Secondary structure (1)
        • 4.6.1.1. Helix (01)
          • 4.6.1.1.1. Effect on left handed protein helix (00)
          • 4.6.1.1.2. Effect on alpha helix (01)
          • 4.6.1.1.3. Effect on Pi helix (10)
          • 4.6.1.1.4. Effect on three ten helix (11)
        • 4.6.1.2. Effect on turns (10)
          • 4.6.1.2.1. Effect on ASX turn (00)
          • 4.6.1.2.2. Effect on ST turn (01)
          • 4.6.1.2.3. Effect on protein beta turn (10)
          • 4.6.1.2.4. Effect on protein gamma turn (11)
        • 4.6.1.3. Beta/Loop (11)
          • 4.6.1.3.1. Beta (0)
            • 4.6.1.3.1.1. Parallel (0)
            • 4.6.1.3.1.2. Anti-parallel (1)
          • 4.6.1.3.2. Effect on Loops (1)
            • 4.6.1.3.2.1. Effect on protein schellman loop (0)
            • 4.6.1.3.2.2. Effect on protein beta bulge loop (1)
        • 4.6.1.4. Others (00)
          • 4.6.1.4.1. Effect on beta bulge (00)
          • 4.6.1.4.2. Coil (10)
          • 4.6.1.4.3. Effect on ST staple (11)
          • 4.6.1.4.4. Unknown (01)
      • 4.6.2. Tertiary structure (0)
        • 4.6.2.1. Local protein conformation change (0000)
        • 4.6.2.2. Global protein conformation change (0001)
        • 4.6.2.3. protein overpacking (0101)
        • 4.6.2.4. Effect on folding rate (0010)
        • 4.6.2.5. Changed domain orientation (0011)
        • 4.6.2.6. N-terminal protein elongation (0100)
        • 4.6.2.7. Generation of a novel post translational modification (0101)
        • 4.6.2.8. Effect on intra transmembrane polypeptide (0110)
        • 4.6.2.9. variation preventing polypeptide processing (0111)
        • 4.6.2.10. protein cavity formation (1000)
        • 4.6.2.11. C-terminal protein elongation (1001)
        • 4.6.2.12. Effect on extra transmembrane polypeptide (1010)
        • 4.6.2.13. Protein truncation change (1011)
        • 4.6.2.14. Deletion of a post translational modification site (1100)
        • 4.6.2.15. Protein fusion - protein elongation (1101)
        • 4.6.2.16. Effect on protein splicing (1111)
    • 4.7. Functional variation (3 bits)
      • 4.7.1. Effect on protein storage (000)
      • 4.7.2. Neomorphic protein variation (001)
      • 4.7.3. Effect on protein information transfer (010)
      • 4.7.4. Effect on protein movement (011)
      • 4.7.5. Antimorphic protein variation (100)
      • 4.7.6. Effect on transport function of protein (101)
      • 4.7.7. Loss of function (110)
      • 4.7.8. Epigenetic changes (111)
    • 4.8. Effect on motif (2 bits)
      • 4.8.1. Effect on protein niche motif (00)
      • 4.8.2. Effect on protein ASX motif (01)
      • 4.8.3. Effect on protein NEST motif (10)
      • 4.8.4. Effect on protein ST motif (11)
  • 5. Variations (18 bits)
    • 5.1. Variation origin (2 bits)
      • 5.1.1. Non-genetic origin (10)
      • 5.1.2. Paternal (00)
      • 5.1.3. Maternal (01)
      • 5.1.4. Both (11)
    • 5.2. Variation size (1 bit)
      • 5.2.1. Streched (1)
      • 5.2.2. Single nucleotide (0)
    • 5.3. Variation type (1 bit)
      • 5.3.1. Synonymous (1)
      • 5.3.2. Non-synonymous (0)
    • 5.4. Experimental classification (1 bit)
      • 5.4.1. Tissue details available (1)
      • 5.4.2. Tissue details not available (0)
    • 5.5. Details (1 bit)
      • 5.5.1. Experimental data available (1)
      • 5.5.2. Experimental data not available (0)
    • 5.6. Geographical details (2 bits)
      • 5.6.1. Yoruba in Ibadan, Nigeria (YRI) (00)
      • 5.6.2. Japanese in Tokyo, Japan (JPT) (11)
      • 5.6.3. Han Chinese in Beijing, China (CHB) (01)
      • 5.6.4. CEPH (Utah residents with ancestry from northern and western Europe) (10)
    • 5.7. Pathogenecity (2 bits)
      • 5.7.1. Repeats disease associated pathogenecity association (00)
      • 5.7.2. Disease causing pathogenecity association (01)
      • 5.7.3. Associated variants disease associated pathogenecitty association (10)
      • 5.7.4. Not related to clinical phenotype pathogenecitty association (11)
    • 5.8. MAF data (1 bit)
      • 5.8.1. Greater than 1% (1)
      • 5.8.2. Less than 1% (0)
    • 5.9. CPV data (1 bit)
      • 5.9.1. Reported (1)
      • 5.9.2. Not reported (0)
    • 5.10. Conservation (1 bit)
      • 5.10.1. Variant (0)
      • 5.10.2. Invariant (1)
    • 5.11. Mesh term (1 bit)
      • 5.11.1. Available (1)
      • 5.11.2. Not Available (0)
    • 5.12. D.rerio (1 bit)
      • 5.12.1. Reported as model (1)
      • 5.12.2. Not reported (0)
    • 5.13. Mus musculus (1 bit)
      • 5.13.1. Reported as model (1)
      • 5.13.2. Not reported (0)
    • 5.14. D.melangoster (1 bit)
      • 5.14.1. Reported as model (1)
      • 5.14.2. Not reported (0)
    • 5.15. C.elegans (1 bit)
      • 5.15.1. Reported as model (1)
      • 5.15.2. Not reported (0)
  • 6. Interactions (11 bits)
    • 6.1. Complex type (2 bits)
      • 6.1.1. Protein-DNA complex (11)
      • 6.1.2. Protein-protein complex (10)
      • 6.1.3. Riboprotein complex (00)
      • 6.1.4. Protein-small molecule complex (01)
    • 6.2.Genetic Interaction (4 bits)
      • 6.2.1. Double non-monotonic genetic interaction defined by inequality (0000)
      • 6.2.2. Non-interactive genetic variation defined by inequality- Neutral genetic interaction (0001)
      • 6.2.3. Additive genetic interaction defined by inequality (1110)
      • 6.2.4. Conditional genetic interaction defined by inequality (0100)
      • 6.2.5. Asynthetic genetic interaction defined by inequality (0110)
      • 6.2.6. Single non-monotonic genetic interaction defined by inequality (0111)
      • 6.2.7. Colocalization (0101)
      • 6.2.8. Suppressive genetic variation defined by inequality - Epistatic genetic interaction (1111)
      • 6.2.9. Association (1100)
      • 6.2.10. Epistatic genetic variation defined by inequality - Epistatic genetic interaction (1101)
      • 6.2.11. Synthetic genetic variation defined by inequality - Negative interaction (1011)
      • 6.2.12. Inequality (1010)
      • 6.2.13. Negative interaction (1000)
      • 6.2.14. Neutral interaction (0011)
      • 6.2.15. Not defined (1001)
      • 6.2.16. Positive interaction (0010)
    • 6.3. Bonds (3 bits)
      • 6.3.1. Common (00)
        • 6.3.1.1. Disulphide bridge-covalent bond (0)
        • 6.3.1.2. Hydrogen bond network (1)
      • 6.3.2. Structural (01)
        • 6.3.2.1. Inter-molecular (0)
        • 6.3.2.2. Intra-molecular (1)
      • 6.3.3. Other (10)
        • 6.3.3.1. Vander waals interactions (0)
        • 6.3.3.2. Hydrophobic interaction (1)
      • 6.3.4. Charged (11)
        • 6.3.4.1. Salt bridge-non covalent bond (0)
        • 6.3.4.2. Electrostatic interaction non-covalent bond (1)
    • 6.4. Interactors (2 bits)
      • 6.4.1. Biopolymer (0)
        • 6.4.1.1. Polysachharide (0)
        • 6.4.1.2. Peptide (1)
      • 6.4.2. Small molecule (1)
        • 6.4.2.1. Metal (0)
        • 6.4.2.2. Water (1)