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...
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™ ...
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 ...
Additional file 2: Table S2. BLAST hits obtained from NCBI blastn using 16S rDNA and gyrB sequences of representative strains belonging to the different Enterobacter agglomerans biotypes defined by Brenner et al. (PDF 19 KB) Authors’ original submitted files for images Below are the links to ...
reesei (Additional file 2) was contructed by mapping T. reesei genes to Aspergillus niger genes by bi-directional best hit blastp [118] with a cut-off of bit score > 50 in either direction ). Metabolic reactions were then transferred for each gene from the A. niger metabolic model [48...
. 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-2 (119 ...
PCR fragments were purified using the Wizard Plus SV kit (Promega, Wallisellen, Switzerland) and sequenced at Microsynth (Balgach, Switzerland). Annotation of the mt genome Open reading frames (ORFs) in the mtDNA sequence of P. subalpina were searched with NCBI orf finder[58]. blastp[59] ...
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 ...
Adaptive designs (ADs) allow pre-planned changes to an ongoing trial without compromising the validity of conclusions and it is essential to distinguish pre-planned from unplanned changes that may also occur. The reporting of ADs in randomised trials is
Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increase