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. ...
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...
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 ...
InT. mongolicusgenome, most syntenic regions exhibited 1:1 relationship (green lines), whereas a minority of blue collinearity blocks exhibited 1:2 relationship (Fig.2a). BetweenT. mongolicusandVitis viniferagenomes, the collinearity relationship was mainly 1:3 (Fig.2c and S3). In the opposite ...
Finally, an enrichment analysis was completed for the sets of up-regulated unigenes in each of the three tissues studied using the corresponding Blast2GO module, which is based on Fisher's Exact Test and FDR statistics. Additional File 6 shows GO terms showing a significantly higher or lower ...
facilitating the prompt initiation of innate immune responses in response to infection through the stringent regulation of BRHIS1. Inhibition of the expression ofBRHIS1exhibited increased resistance to blast pathogens in rice, suggesting the negative regulatory role of BRHIS1 in plant immunity. After ...
n=3, NC: Normal control Full size image Discussion IT is well established that blastema formation results from the dedifferentiation of the differentiated cell types on the amputation plane back to embryonic-like cells (Mescher 1996), but these cell types retain the memory of their origin when ...
Blast2GO with NR annotation to obtain the GO annotation; InterProScan5 to obtain the InterPro annotation; and TransDecoder (v 3.0.1, Brian Haas, San Francisco, CA, America) to identify the candidate coding area. The longest open reading frame (ORF) was extracted, and then the coding regio...
(492 up-regulated and 983 down-regulated) were detected in hybrid crabs with displaced eyestalks (DH). The most significant DAS events and DETs were annotated as being endoplasmic reticulum chaperone BiP and leucine-rich repeat protein lrrA-like isoform X2. In addition, the top ten significant...
Alternatively, the user can use a preferred protein sequence to search the whole set of TFs in PlnTFDB@Uni-Potsdam, or the species-centered databases, using BLAST. The availability of all members of a family in several species will facilitate the study of their biological functions, phylogenetic...