A novel feature of these vectors is that they contain a universal multiple cloning site, which enables more than 99% of the rice coding sequences to be conveniently transferred between vectors.
To facilitate the transfer of rice fragments between vectors, we analyzed the restriction enzyme recognition sites in the rice coding sequences (CDSs) based on the MSU RGAP database Version7 (http://rice.plantbiology.msu.edu/), and we then synthesized a powerful universal MCS suitable for cloning of more than 99% of rice CDSs.
For negative samples, we used rice coding sequences, which were downloaded from TIGR Rice Genome Annotation Database [ 64].
For comparison, the rice coding sequences [ 36] contained 51,437 sequences with 3,265 unique domains.
Both the wheat contigs as well as rice coding sequences were compared to these domains using NCBI BlastX (E-value ≤ 10-3).
BLAST hits with E-values less than e-40, were retrieved and used to query rice coding sequences at the Rice Genome Annotation Project database [ 33, 34].
The Arabidopsis and rice coding sequences were downloaded from the TAIR web site [ 69] and the Rice Genome Annotation Database from TIGR [ 70], respectively.
14005 rice coding sequences that are longer than 75 codons were obtained from Gramene database [ 16] and the EMBL as previously described [ 17].
(PDF 45 kb) Additional file 6: Is a table listing rice coding sequences (including and excluding TE) and cDNA with wheat unigenes at different e-values.
Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences.
Accordingly, Mukhopadhyay et al. (2008) suggested that GC-rich and GC-poor rice coding sequences may experience different selective pressures, suggesting these genes should be analyzed separately.
