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Table 1 Ortholuge-ratios can help predict which gene in a given putative orthologous group is likely a paralogaa.

From: Improving the specificity of high-throughput ortholog prediction

Ratio1

Ratio2

Ratio3

Probable Paralog

a

Ingroup1 paralog

a

↓

Ingroup2 paralog

↓

↓

-

Outgroup paralogb

or c

or c

variable d

Ingroup1 & Ingroup2 paralogs

↓

variable d

Ingroup1 & Outgroup paralogs

variable d

↓

↓

Ingroup2 & Outgroup paralogs

  1. a Only selected scenarios are listed. Arrows indicate relative increases or decreases in a ratio value, when compared to the highest frequency values in a histogram plot (i.e. "expected" ratio value). Smaller arrows indicate that the increase is less. In the case of the ingroup1 or ingroup2 paralog scenarios, it will depend on how divergent the paralog is and how distant the outgroup is.
  2. b Note that an outgroup paralog cannot be discriminated from cases of orthologs, nor does this analysis need to discriminate such cases (see text). However, this has been included in the table solely to illustrate how ortholog paralog cases can be discriminated (using Ratio 3) from cases where there is a combination of an ingroup1 (or ingroup2) paralog and an outgroup paralog.
  3. c This scenario will resemble an ingroup1 paralog scenario or ingroup2 paralog scenario, if one of the two ingroup paralogs diverged much more than the other.
  4. d The variation may be an increase or decrease, depending on which of the two paralogs is more diverged. Ratio 3 can help resolve such cases.