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...
Despite the knowledge that the soil–plant–microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how the agriculturally important symbiosis of
Pan-genome analysis of Methanomassiliicoccales.APCoA showing the genomic divergence based on the gene orthologs of these 243 genomes plus five outgroup taxa from the order Thermoplasmatales and colored by their assigned genus. ANOSIM tests were used to assess the significance of dissimilarities betw...
file of a related genome with Liftoff 1.6.1 [43]. With additional input data, the pipeline can detect ectopic mitochondrial and apicoplast sequences using BLAST 2.10.1 [34], and RNA-Seq read coverage using HISAT2 2.2.1 [44]. If the user provides proteome FASTA files of species that ...
MCScanX [103] was used for syntenic region detection with the all-to-all BLASTP results (blocks with at least 10 pairs homologous genes and the gap was less than 5 genes) for orange/mango, orange/longan, mango/longan, and mango/mango. TheKsbetween the syntenic homologous gene pairs was ...
Functional enrichment using gene ontology terms and Fisher's Exact Test was performed using Blast2GO for the sets of up-regulated unigenes in each of the three tissues (bean, leaf and flower). The full set of unigenes of the PUCE CAFE array was used as the reference set. The resulting ...
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
Different concentrations (2, 5, 10 nM) of DHT were applied for 24 h. Value: mean ± S.E.M. 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 ...
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...