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Ensembl Gene Id, orthologous relationships, locations in base pair for each species were downloaded and deposited into a MySQL database (v.4.1.12).
We determined the number of reads mapping to each gene with Bowtie, normalized read count by gene length, and tallied the number of reads per base pair for each gene in each functional category/pathway to obtain a proxy for the total amount of expression.
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A comparison was performed with 17 markers across the Saltol region and 61 SSRs across the background on seven Pokkali accessions (IRGC 8948, 15388, 15602, 15661, 26896, 28609, 108921) and IR29, FL478, NIL-17, and NIL-30 by scoring allele sizes in base pairs for each gel picture.
Diagnostic base pairs (or combination of base pairs) for each species within the Malagasy region are presented.
Then, average density of TEs was estimated as percentage of base pairs for each range of 50 Kb occupied by TEs.
GenomeScanner reports the position of each identified FRT-like sequence both within the sequence contig files and within a chromosomal fragment map based on linear order of files for each chromosome and the cumulative base pairs for each chromosome (Figure S1).
The total numbers of base pairs for each sub-region were summed.
Control siRNAs were designed by substitution of two base pairs for each sequence.
To calculate the non-conserved non-repeat base pairs, the non-conserved repeat base pairs were subtracted from the total non-conserved base pairs for each sub-region.
We observed the same sized length variants (i.e. the size of deletion in base pairs) for each marker that were found in [ 47, 48] (Table 1).
This was done by taking the union of exonic base pairs for each group of transcripts arising from the same gene.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com