A Genotyping by Sequencing method

Restriction Enzyme Sequence Comparative Analysis (RESCAN)


Feb 6 2012. We are updating this site for the forthcoming publication in BMC Genomics. All links should be live by end of April 2012.


  • Bench method
    • The protocol for RESCAN library construction
    • Hints and Troubleshooting
  • Software
    • Restriction enzyme analysis. For planning purposes one needs to know how many and of what size fragments are produced by the digestion of a genome with one or more restriction enzymes.  In Silico Digestor takes a genome as a fasta file and one or more restriction enzyme sites. It outputs a table of fragments and corresponding sizes. It requires Python 2.6-2.7.
    • Barcode generator for RESCAN adapters.
    • MAPS Mutations And Polymorphism Survey, a pipeline for mutation discovery and genotype analysis. This software takes barcoded sequence reads from many individuals and processes them. It sorts them and filters them according to user criteria, aligns them to a reference genome using BWA, extracts the changes from the mpileup table of BWA, compares them across to multiple individuals, and makes change calls according to user-determined criteria. The output is a large table that can be further parsed in Excel, JMP-SAS, or by a custom script to yield genotypes or mutation calls.


The sequence reads used for mutation discovery in rice var. Kitaake have been deposited in the NCBI Short Read repository with accession number SRA049884.2

RESCAN publications

  • Monson-Miller J, Sanchez-Mendez D, Fass J, Henry IM, Tai TH, Comai L. 2012. Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. BMC Genomics
  • Seymour DK, Filiault DL, Henry IH, Monson-Miller J, Ravi M, Pang A, Comai L, Chan SWL, Maloof JN. 2012. Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping. Proc Natl Acad Sci U S A.
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