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BLAST plus: architecture and applications. BMC Bioinformatics. 2009;10:421. Article PubMed PubMed Central Google Scholar Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb). 2021;2:100141. ...
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...
The sequence alignment of species annotation was performed using BLAST and the alignment databases SILVA and NT-16S. LEfSe was performed to detect significantly different abundances for designated taxa of the gut microbiome using a Kruskal – Wallis rank sum test, and bioinformatics analysis was ...
Finally, we compared taxonomic assignments with known fauna of Slovenia [97] to replace non-regional species identified with BLAST with closely related regional taxa. This was necessary for some rodents that assigned to related congeners or confamilias sometimes with 100% match. All statistical analys...
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...
BlastP is then used to relate the resulting amino acid sequences to a protein database. The ORF from each transcript with the best hit to the database is then selected as the predicted true ORF. Using the ORF information, the transcripts are then labeled with attributes based on the ...
2009). Therefore, a blastema consists of multiple different cell types, which has been confirmed by recent studies using scRNA-seq (Gerber et al. 2018; Leigh et al. 2018; Li et al. 2021). Deer antlers are the only case of mammalian epimorphic full regeneration, which is realized through...
BLASTP (E-value less than e-20) searches against non-redundant GenBank® CDS translations were used to establish biological informative names for sequences without descriptions. Sequences that contained only motifs incompatible with peroxisomal localization (e.g., RNA-helicase (IPR0006050)), or...
The myeloblastosis (MYB) transcription factor (TF) family is one of the largest and most important TF families in plants, playing an important role in a life cycle and abiotic stress. In this study, 268 Avena sativa MYB (AsMYB) TFs from Avena sativa were