SOOP (System for Optimized Overgo Picking) is a tool for the design and selection of overgo probes optimized for high-throughput comparative mapping. Soop designs “overgo” DNA hybridization probes either from a sequence comparison or a straight FASTA file. The basic idea behind designing probes from sequence comparisons is that orthologous sequences between two species that are highly concerved are likely to also be conserved in a third species. Soop runs in these two modes depending on the type of file passed to it as the last parameter on the command line.
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Thomas, J.W., Prasad, A.B., Summers, T.J., Lee-Lin, S.Q., Maduro, V.V., Idol, J.R., Ryan, J.F., Thomas, P.J., McDowell, J.C., Green, E.D. 2002.
Parallel construction of orthologous sequence-ready clone contig maps in multiple species.
Genome Res. 12(8):1277-85.