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Database resources and bioinformatics tools used in this study
Gramene
http://www.gramene.org/
Genetic maps, integrated maps, contigs, and published genetic markers
NCBI
http://www.ncbi.nlm.nih.gov/
Nucleic acids sequences of BACs/PACs, GenBank sequence annotation and marker
information
Beijing Genomic Institute
http://rise.genomics.org.cn/rice/index2.jsp
Genome sequence of Oryza sativa ssp. indica cv. 93-11
International Rice Genome
Sequencing Project (IRGSP)
http://rgp.dna.affrc.go.jp
Genome sequence (chromosome 1, 2, 6, 7, 8 & 9) of Oryza sativa ssp.
japonica cv. Nipponbare
The Institute for Genomic Research
http://www.tigr.org/tdb/e2k1/osa1
Genome sequence (chromosome 3, 10 & 11) of Oryza sativa ssp.
japonica cv. Nipponbare, and annotation resource
BLASTN [20]
http://www.ncbi.nlm.nih.gov/BLAST/
Comparison of a nucleotide query sequence against a nucleotide sequence
database
OvergoMaker 40
http://www.genome.wustl.edu/tools/index.php?overgo=1
Overlapping oligonucleotide probe design
BLAST 2 Seq [16]
http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html
Sequence pairwise comparison of a nucleotide query sequence against another
nucleotide sequence
Oligos
http://www.biocenter.helsinki.fi/bi/bare-1_html/oligos.htm
Tool for making complement, reverse complement, inverted strand, etc.
OligoAnalyzer 3.0
http://scitools.idtdna.com/scitools/Applications/OligoAnalyzer/
Analysis of oligonucleotide sequences
Primer3 [15]
http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi
Primer design
Tandem Repeat Finder
http://tandem.bu.edu/trf/trf.html
Localization and display of tandem repeats in DNA sequence
Repeat Masker
http://www.repeatmasker.org/
Identification of repetitive DNA sequences
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