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This strategy is conceptually similar to the popular tools like BLAST [39] for sequence alignment or our previous strategy scLearn et al. for automatic cell type annotations using single-cell transcriptomic references [24, 25, 30]. In the case of SpaDo, it performs a search by measuring the...
For each putative site, we sorted the pool of BLAST hits by subject strand (in this case, “subject” refers to our plant reference genome) to find which of the paired reads were associated with either the plus or minus strand. Because the transgene-containing end of the amplicon is closes...
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Phytophthora root rot caused by the oomycete Phytophthora capsici is the most devastating disease in pepper production worldwide, and current management strategies have not been effective in preventing this disease. Therefore, the use of resistant variet
Protein structural class predicting is a heavily researched subject in bioinformatics that plays a vital role in protein functional analysis, protein folding recognition, rational drug design and other related fields. However, when traditional feature ex
based on a similarity search against a reference database such as the NCBI-NR database of non-redundant protein sequences [1], usually employing a variant of the BLAST program [2], or on the protein domain search against a protein family database such as PFAM [3]. This is mainly ...
Sea snakes underwent a complete transition from land to sea within the last ~ 15 million years, yet they remain a conspicuous gap in molecular studies of marine adaptation in vertebrates. Here, we generate four new annotated sea snake genomes, thre
ranges contract when adaptation fails [3,7,8]. During this process, the adaptability of edge populations may be constrained by gene flow from the larger core population [3] and the accumulation of deleterious mutations [9]. Therefore, to some extent, accelerating the generation of adaptive innov...
Additional file 3: Supplemental Table 2. Daphnia genes annotated as signaling proteins and other regulators based on sequence conservation with Drosophila genes with known functions. Scores are reported from results obtained by Blastx against all predicted translations from version 4.2.1 of the D. mel...