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Our evaluation covered three key perspectives: (1) spatial domain detection on single-cell spatial transcriptomics data, (2) spatial domain detection on spot resolution spatial transcriptomics data, and (3) TLS-like domain detection. For the first test (Fig. 2a), we can see that SpaDo ...
It utilized PSI-BLAST [2] to extract evolutionary information from protein representations as input. DPPI was known as the first deep learning model to achieve state-of-the-art performance in binary PPI prediction. Another approach, PIPR [3], utilized a Siamese architecture and a residual ...
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...
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 ...
Map of central metabolic pathways inR. toruloidesBOT-A2. Pathways were reconstructed from genome and RNAseq data, using KEGG, SGD and BLASTp. The network includes glycolysis (pink), the pentose phosphate pathway (blue), the TCA cycle (pale yellow), lipid biosynthesis, triacylglycerol biosynthesis...
Explaining contrasting patterns of distribution between related species is crucial for understanding the dynamics of biodiversity. Despite instances where hybridization and whole genome duplication (WGD) can yield detrimental outcomes, a role in facilita
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Clearly, the key of the wavelet denoising method is undoubtedly to select the value of threshold and threshold function, which has the greatest impact on the effect of wavelet denoising. There are generally three ways to select the value of threshold: default threshold, given threshold and forced...
We characterized all thousand base pair windows without aligned reads using a BLASTn search against the “nr/nt” database. In order to identify high-confidence sequence differences across the Haitian and Dominican Republic isolates, we used Fisher’s exact test based on counts of reads aligned ...