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Its alignment to sorghum sequence was puzzling because the six genes aligned to different regions of the sorghum genome.
The CAZy family profile was calculated by summing the relative abundance of genes aligned to it.
Mouse genes aligned to the same human gene were considered to be candidate inparalogs and formed duplication families.
Regardless of tissue type, most of the small RNAs mapping to protein coding genes aligned to 5'- and 3'-UTRs.
Over 80% of the OGSv3.2 genes aligned to both the Aflo_1.0 and Bter_1.0 genome assemblies (Table 5).
Expression of over 30 000 genes, aligned to the apple genome, was monitored, with clear divergence of expression among treatments after 1 day of CA storage.
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In several cases, multiple isoforms of one gene aligned to the human genome so only one transcript with the lowest eValue for alignment was kept.
When we performed the same analysis for our candidate autosomal genes (3,664 genes), 2,111 aligned to autosomal scaffolds and only 337 (14% of aligned genes) mapped to the Z-linked scaffolds.
For each pair, the gene copy aligned to outgroup genes in the whole-genome alignment was designated as the parent, and the copy that did not align to any regions of the outgroup genomes was considered the child.
The four pgip genes align to each other, and alignment extending beyond the coding regions was observed only between PvBpgip1 and PvBpgip2 and between PvBpgip3 and PvBpgip4 (Additional file 8).
After discarding 18 S and 28 S ribosomal RNA genes and alpha-tubulins, 124 known genes were aligned to the 90e sequences.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com