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Segmental duplication analysis was done with the RGAP rice segmental duplication database with the maximum length distance permitted between collinear gene pairs set to be 500 kb.
Segmental duplication analysis was done with DAGchainer [ 60] and the TIGR rice segmental duplication database (please see Availability & requirements for more information) with the maximum length distance permitted between collinear gene pairs set to be 500 kb.
The GST genes present on duplicated chromosomal segments were identified by segmental genome duplication of rice available at RGAP with the maximum length distance permitted between collinear gene pairs of 500 kb.
The GRX genes present on duplicated chromosomal segments were identified by segmental genome duplication of rice available at RGAP with the maximum length distance permitted between collinear gene pairs of 500 kb.
The full list of homologous sequences found in segmental duplicated regions were downloaded from the TIGR web site with a maximum length distance permitted between collinear gene pairs of 100 kb for Oryza sativa [ 57] and Arabidopsis thaliana [ 58] respectively.
The presence of OsPTR genes on duplicated chromosomal segments was investigated by searching the segmental genome duplication of rice at MSU RGAP http://rice.plantbiology.msu.edu/segmental_dup/index.shtml with the maximum length distance permitted between collinear gene pairs of 500 kb.
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Finally, the third mode builds trees derived from all subword distances for various maximum lengths.
For interstitial LOH events, the tract length was calculated as the average of the maximum tract length (the distance between the heterozygous SNPs flanking the LOH region) and the minimum tract length (the distance between the first and last homozygous SNP in the conversion tract).
For conversions associated with crossovers, the length was the average between the maximum tract length (the distance between the last heterozygous SNP before the conversion tract and the SNP that has the reciprocal LOH pattern indicative of the crossover) and the minimum length (the distance between the first and last homozygous SNPs of the tract).
Both total corallith abundance and the frequency of larger coralliths (maximum lengths of >1 m) increased with distance from the shore (Fig. 2).
Tree topologies were evaluated by reconstructing phylogenies using maximum likelihood evolutionary distance analysis (Phylip Distance Method with Jukes and Cantor model) of aligned near full-length sequences (>1200 bp).
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