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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...
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The differentially expressed transcripts were annotated based on the NR, Swiss-Prot, Pfam, GO, KEGG, COG, eggNOG, and KOG databases, using BLASTX algorithms with a significant threshold E-value < 1e-5. To optimize the genome annotation information and discover new transcripts and genes, ...
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...
unknown were discarded. A specific sequence similarity search using the Basic Local Alignment Search Tool (Blast), available on the National Center for Biotechnology Information (NCBI) platform, was performed for the most dominant ASV (ASV00001) to assess whether or not it belonged to the already...
The nlme [51] library available in the R [52] software was used for the statistical analysis. Follow up comparative sequence analysis for specific peptides was done using BLAST 2 sequences alignment and ClustalW.Abbreviations C1: Principal component 1 C2: Principal component 2 CRMP-2: ...
Genes closely linked to Scn1b on the mouse chromosome were compared to this region of the zebrafish genome using the Blast program. Predicted genes for zebrafish orthologs were then mapped against the zebrafish Zv6 assembly [20] to determine their linkage group designations. Located in close ...
(Additional file2: Fig. S6). One introgression occurred betweenC. fugongensisand the ancestor of the japonica-corniculata clade plusC. fugongensis, with a BS value of 84%, where the ancestor contributed 23.6% of genetic material toC. fugongensis(Fig.3e). It is worth noting that such ...
Quezon city for capillary sequencing. Their results were processed using DNA Baser Assembler v4, and were trimmed and cleaned using BioEdit v7.2 [46]. The final sequences were subjected to the Basic Local Alignment Search Tool (BLAST) of the National Center for Biotechnology Information (NCBI) ...