Expert opposes full-scale blast testCam Fortems
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...
BLAST2GO [75] was used to obtain the associated GO terms. The enrichment score is defined as the hypergeometric test value [76]. Whole genome duplication analysis The all-against-all BLASTP method (E value < 1e−5) was used to detect paralogous genes in pistachio, C. sinensis, ...
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
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™ ...
The search for sex determination genes in flounder is critical to understanding the mechanisms controlling sex determination, which may have significant implications for controlling sex ratios in aquaculture and improving breeding programs. The BLAST 2.2.29 algorithm was used to retrieve the genomic sequen...
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...
We used BLASTP and HMMER3.1 in the entire rose genome to discover AP2/ERF members. All potential rose proteins were then subjected to domain analysis to confirm the presence of the AP2 protein domain (PF00847). Eventually, a total of 135 AP2/ERF family members were identified in rose. ...
Finally, using AtRCC1s sequence as a query to search the soybean proteome (BLASTP), proteins that met the BLASTP threshold conditions (E-value ≤1e-5 and identity ≥50%) were retained as the final GmRCC1s and AtRCC1s family members. PI and MW were analyzed by the Compute PI/MW tool...