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EST alignments of mapped markers in the RH map were performed using TBLASTX searches against the cDNA database of zebrafish (Danio rerio), medaka (Oryzias latipes), three-spined stickleback (Gasterosteus aculeatus) and green-spotted pufferfish (Tetraodon nigroviridis) at Ensembl [ 56].
Heat map, senior bubble map, scatter plot map and venn map were performed using the OmicShare tools, a free online platform for data analysis (www.omicshare.com/tools).com/tools
All projections of QTL onto the consensus map were performed using the Biomercator (2.0) (http://www.genoplante.com/).com/
All of the calculations for the creation of the integrated map were performed with the Biomercator software, version 2.1 [ 14].
The characterization of this genetic map and the comparative analysis with a previous integrated consensus map were performed.
Comparisons between groups using SAM, and unbiased analysis of the entire dataset using singular value decomposition and self-organizing map were performed.
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The intergroup comparison of the FiCD map was performed using vertex-wise multi-subject statistical analysis.
The overlapping of AM transcriptome map with the AM mutation map was performed by Caryoscope.
The construction of an SNP clustering map was performed using Circos [ 42].
For the first time, a comprehensive annotation of regulatory RNAs in MAP was performed.
Assays of ANTS/DPX release and NBD-based fluorescence mapping were performed as previously described.
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