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...
, and during the second test, the building was enclosed with a blast-resistant façade. The applied blast loads were similar for both tests. During the first test, the frame responded elastically with no failure on the LFRS, while the glazed façade almost completely shattered. The blast-...
Then, the blastx results were analyzed using the longReads LCA algorithm of MEGAN [33]. RNA sequencing and data analysis Total RNA from the colonic tissue was extracted and purified using TRIzol reagent (Invitrogen). Only those samples with RIN > 7 were used for RNA-seq. TruSeq™ ...
While some previous methods also align to the virus first [97], either the software no longer appears available where specified at publication [98, 99], or they use BLAST [100, 101] instead of a faster short read aligner [102]. Unlike ViFi [58], Polyidus requires that the chimera ...
In brief, all possible SPL proteins were identified using the BLASTp algorithm (score value ≥ 100, e value ≤ 1e-10) with the trihelix protein sequence of Arabidopsis used as the reference sequence. The obtained SPL protein sequences were then converted into a Hidden Markov Model ...
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...
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
(a subset of those included here) produced a phylogeny for those 10 taxa based on 1507 single-copy orthologs identified through a combination of, "(i) protein-protein pairwise reciprocal BLAST (blastp); (ii) reciprocal protein genomic sequence best match (tblastn); and (iii) Darwin pairwise...
In particular, we predict the contact vector of protein structures using an artificial neural network based on position-specific scoring matrices generated by PSI-BLAST and align these predicted contact vectors. The resulting sequence alignments are assessed using two different tests: First, we assess ...
(Table2). The NCBI BLAST results of amplicon nucleotide sequences of these bands yielded 100% identity matches. Likewise, the positive controls with their expected gel bands for DENV-1 (482 bp), DENV-3 (290 bp), and DENV-4 (392 bp) isolated from the localAe. aegypti, and for DENV-...