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Note that sfApaf-1 has a long deletion in each propeller domain compared with Apaf-1 of other animals.
We designed experiments to determine if long deletion mutations were the consequence of the repair (misrepair) of DNA double-strand breaks.
–-gape-max-occ Maximum occurrextending extending a long deletion in BWT querying [ default: 10 ]. –-penalty-mismatch Mismatch penalty for querying involving BWT [ default: 3 ].
(5) Ionizing radiation produces more long deletion mutations than does UV radiation and, similarly, ionizing radiation produces more DNA double-strand breaks than does UV radiation.
Therefore, numerous primary DNA double-strand breaks would be concentrated at a nearby Chi site, thereby enhancing or diminishing the apparent yield of long deletions per double-strand break, depending upon the location of the Chi site relative to the position of a break needed for the initiation of the recombination event required to produce a long deletion mutation (A131).
The average length of structural variants was as follows: 1.5 Mbp for inversion, 59.4 kbp for tandem duplication, 101.3 kbp for long deletion, 1.7 kbp for long insertion.
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–-log-gap logapcaled gapenaltyty for long deletions for querying involving BWT.
The formation of long deletions is linear with dose, as is the formation of DNA double-strand breaks.
In our mutation studies (A131), we found that a recB mutation completely blocked the formation of long deletions, while base substitution and frameshift mutations were little affected.
In addition, physiological conditions that enhance the ability of cells to repair DNA double-strand breaks (i.e., conditions of MDR) also enhanced the yield of long deletions.
A structural variant detection tool Manta version 1.1.1 (Chen et al. 2016) was employed for calling translocation breakends, inversions, tandem repeats, long insertions and long deletions with the default condition.
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