PMC:3091640 / 36249-37938 JSONTXT

{"project":"2_test","denotations":[{"id":"20646326-17145706-10480767","span":{"begin":177,"end":179},"obj":"17145706"},{"id":"20646326-12519987-10480768","span":{"begin":336,"end":338},"obj":"12519987"},{"id":"20646326-9514730-10480769","span":{"begin":643,"end":645},"obj":"9514730"},{"id":"20646326-12520028-10480770","span":{"begin":862,"end":864},"obj":"12520028"},{"id":"20646326-10592173-10480771","span":{"begin":1526,"end":1528},"obj":"10592173"},{"id":"20646326-11181991-10480772","span":{"begin":1685,"end":1687},"obj":"11181991"}],"text":"All the annotated gene and protein sequences of rice chromosomes (TIGR release 6) were downloaded from The Institute for Genomic Research (TIGR) Rice Genome Annotation website [39]. For Arabidopsis, all the annotated gene and protein sequences (TAIR release 8) were downloaded from The Arabidopsis Information Resource (TAIR) database [40]. The redundant and genes annotated as transposable elements were removed to get a final list of non-redundant genes in rice and Arabidopsis. To identify DRR genes we used two different criteria. To select the correct putative orthologue first, we performed global alignments using the FASTA BLAST suit [41] and rejected all alignments with less than 20% identity, unless a portion of the protein showed a very strong similarity. Secondly, a possible conserved motif was searched using the Conserved Domain Database (CDD) [42]. When none of these two approaches produced significant result, the corresponding gene was discarded. Primarily, Potential DRR genes in rice and Arabidopsis genome were identified by sequence similarity searches using the DNA repair genes of human, Saccharomyces cerevisiae and E. coli as seed sequences orthologs and keyword searches. Secondly Arabidopsis DRR genes were used to identify the putative DNA repair genes in rice genome. We, next, we searched the primary literature, and when presented, included experimental results that concerned to plant systems to authenticate the annotation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database [43] was used as guide for the gene involve in main repair and recombination pathway while we follow the classification of Wood et al. for the DNA repair genes[44]."}