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1 # chromeister
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2 An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.
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3
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4 ## Requirements
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5
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6 GCC compiler (any version that is not completely outdated should do) and the R-base package (default R installation should do) with no extra packages.
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7 Simply download the .zip and unzip it, or clone the repository (currently the active branch is "histo-kmer-ultra" DO NOT USE ANY OTHER).
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8 Then issue the following commands:
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9
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10 cd chromeister/src && make all
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12 You are ready to go!
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13
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14 ## Use
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15
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16 There are several ways in which CHROMEISTER can be used. The simplest one is to run a 1-vs-1 comparison and then compute the score and the plot.
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17 To do so, use the binaries at the bin folder:
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19 CHROMEISTER -query seqX -db seqY -out dotplot.mat && Rscript compute_score.R dotplot.mat
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21 This will generate the comparison matrix, the plot of the comparison with the automatic scoring and the guides to be used in an exhaustive GECKO comparison.
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23 More to be added soon!
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