Table 1.
Comparison of existing in-silico rSNP detection tools
| Method | Allele-specific scores | P-values for allele-specific scores | Between-allele scores | P-values for between-allele scores | User specified motif library | Scalability to >20 K SNPs | Visualization of SNP effects | Open source code |
|---|---|---|---|---|---|---|---|---|
| atSNP | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| is-rSNP (Macintyre et al., 2010) | ✓ | ✓ | ✓ | ✓ | ✓ | |||
| RAVEN (Andersen et al., 2008) | ✓ | ✓ | ||||||
| rSNP-MAPPER (Riva, 2012) | ✓ | ✓ | ||||||
| TRAP⋆ (Thomas-Chollier et al., 2011) | ✓ | ✓ | ✓ | |||||
| FIMO⋆⋆ (Grant et al., 2011) | ✓ | ✓ | ✓ | ✓ |
⋆TRAP takes as input only one SNP at a time.
⋆⋆FIMO scans sequences for occurrences of motifs and is not readily a rSNP tool.