Sentence examples for maize sequences were from inspiring English sources
Maize sequences were identified by local BLASTP program as described above.
Transcripts with best matches to viral or maize sequences were removed from further analyses.
The maize sequences were manually annotated using homology searches in various GenBank databases with multiple BLAST programs [ 57].
Finally, maize sequences were used as queries against the NCBI database to check that they correspond to the initial rice transcript flanking the Route66 insertion.
To establish potential functions encoded by the memory response genes, the maize sequences were searched against annotated gene models for A. thaliana.
Maize sequences were downloaded from http://www.maizesequence.org (Release 5b.60) and from the Grassius Grass Regulatory Information Server (http://www.grassius.org/index.html).html
The sister clad, containing the rice, B. distachyon, wheat, sorghum and maize sequences, was also highly supported (100%).
The ab initio identification of LTR retrotransposons within the rice and maize sequences was performed by the LTR_STRUC software [ 9] using standard specifications.
Furthermore, most of these maize sequences are derived from the low-to-middle repetitive LTR retrotransposons and not from the very high copy-number elements that have been responsible for doubling the size of the maize genome in the past 5-6 million years.
In a sequence comparison of the adh1-orthologous regions of maize and sorghum, two species that last shared a common ancestor about 12 mya [80], a 212-kb maize sequence was found to be largely collinear with a 66-kb sorghum sequence [84].
The reference element in question is PREM2_ZM_I (from R EPB ASE U PDATE), and hits to this reference element along the maize sequence are highlighted in magenta.
