Estimation of Syntenic Spans between Maize and Rice

The source data for the analysis were;

• Zea mays Agarose FPC Map
• AGI 25 Oct 2004 release
• Oryza sativa (japonica) pseudomolecule assembly
• TIGR release 3
• Zea mays EST sequences
• Retrieved from GenBank
• Zea mays clustered EST sequences (unigenes)
• DuPont/MMP/Incyte 'Cornsensus'

EST clusters and EST singletons attached to the maize FPC map were identified via correspondence with overgos placed on the map as physical markers. Of these sequences, only those that hit an FPContig through multiple clones (BACs) were considered for further analysis.
 
The sequences associated with the resulting list of overgos were aligned to the rice pseudomolecule assembly using BLAT (with parameters -minIdentity=50 followed by PslReps with -singleHit). The alignments were further filtered using the following criteria;

• Alignment length was greater than 150 basepairs and,
• Sequences with more than 3 hits to the genome of equal value were discarded.

The alignments were used to construct a sorted pairwise list of locations on the maize FPC map and their corresponding locations on the rice genome. For each location on a given maize FPContig, if the distance between adjacent points on rice fell within a distance of 300kb, a syntenic span was constructed.