PMC:3091640 / 37940-39889
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3091640","sourcedb":"PMC","sourceid":"3091640","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091640","text":"Analysis of DRR genes\nThe percentage of amino acid identity between a given human/Saccharomyces cerevisiae/E. coli gene and its corresponding orthologue in Arabidopsis and rice was obtained from the Smith-Waterman alignment between the two sequences. Means were calculated using these values.\nDuplicated genes and their Ka, Ks and e-values in DRR proteins of rice, Arabidopsis, sorghum and populus were extracted out from the Plant Genome Duplication Database (PGDD) [45]. PGDD is a public database to identify and catalogue plant genes in terms of intra or inter-genome syntenic relationships.\nPhylogenetic trees were generated for a group of DNA repair protein homologs. Protein sequences were aligned using the Clustal W multiple sequence alignment program [46]. Only unambiguously aligned positions (excluding poorly conserved and gap regions) were used in phylogenetic analysis, which was performed using the MEGA4 [47]. Neighbor-Joining and Parsimony methods were used for phylogenetic tree searching and inference. The phylogenetic trees were tested by bootstrap analysis with 10000 replications and strict consensus trees were constructed. Similar topologies were found for both algorithms employed, and only Neighbor-Joining being displayed. We used PGDD naming convention for the populus and sorghum dataset in this analysis as the original naming style for predicted models were un-informative. The respective accession numbers used in this analysis and the original naming of predicted genes are given in Additional file 9.\nFunctional diversity of DRR proteins was carried out according to the GO rules using the gene ontology tools at http://www.agbase.msstate.edu. Only two independent sets of ontologies were used to describe a gene product: (1) the biological process in which the gene product participates and (2) the molecular function that describes the gene product activities.\nAdditional methods are given in Additional file 10.","divisions":[{"label":"title","span":{"begin":0,"end":21}},{"label":"p","span":{"begin":22,"end":292}},{"label":"p","span":{"begin":293,"end":594}},{"label":"p","span":{"begin":595,"end":1535}},{"label":"p","span":{"begin":1536,"end":1897}}],"tracks":[{"project":"2_test","denotations":[{"id":"20646326-18436778-10480773","span":{"begin":468,"end":470},"obj":"18436778"},{"id":"20646326-7984417-10480774","span":{"begin":761,"end":763},"obj":"7984417"},{"id":"20646326-17488738-10480775","span":{"begin":921,"end":923},"obj":"17488738"}],"attributes":[{"subj":"20646326-18436778-10480773","pred":"source","obj":"2_test"},{"subj":"20646326-7984417-10480774","pred":"source","obj":"2_test"},{"subj":"20646326-17488738-10480775","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#eccf93","default":true}]}]}}