is valuable for providing animal protein to the increasing human populace and also can be used as an excellent animal model for scientific research [1]. Since the domestication of the red jungle fowl, hundreds of phenotypically distinguishable domestic chicken breeds have diverged under the combined ...
Most human protein-coding genes are expressed as multiple isoforms, which greatly expands the functional repertoire of the encoded proteome. While at least one reliable open reading frame (ORF) model has been assigned for every coding gene, the majority of alternative isoforms remains uncharacterized ...
with a periplasmic domain dominated by predicted alpha helical domains (Fig.2a,b) [8,16,17]. The alpha helices have a high propensity to form coiled-coils resulting in the periplasmic domain of Rz to be essentially divided into two coiled-coil domains, CC1 and CC2,...
Well-studied cases of NLRs with integrated domains (NLR-IDs) includeArabidopsis thaliana RRS1(NLR-WRKY) andOryza sativa RGA5(NLR-HMA). Both NLR-IDs require an additional genetically linked NLR,RPS4, andRGA4, respectively, for the activation of disease resistance [5,10,11]. TheRGA4/RGA5and...
The pan-genome ofB. cereus s. l.was inferred with Roary [30] version 3.7.0. TheBCSL_114Prokka annotations were provided to Roary as input; in turn, Roary produced a gene presence/absence matrix (Additional file2), a multi-FASTA alignment of core genes using PRANK [31] version 0.140603,...
(in absolute value) in the dKD vs. control comparison and a change in the opposite direction in the rescue vs. dKD comparison. For each category of events, we also distinguished two subclasses, depending on whether the 'inclusion' or 'exclusion' form of the event is enhanced when NMD is ...
Usage of RootDigger is straight-forward. All that is required is a tree in newick format, and a MSA in either PHYLIP or FASTA format. RootDigger is open source, released under the MIT license, and written in C++, and is targeted at the Linux platform. The code, documentation, test suit...
With data processing module, KBCommons processes uploaded data and imports these data to an appropriate database according to genome version, type of dataset and other customized options. KBCommons supports various standard file formats only including Fasta format for sequences data, FPKM or read ...
Vitis vinifera berry development is characterised by an initial phase where the fruit is small, hard and acidic, followed by a lag phase known as veraison. In the final phase, berries become larger, softer and sweeter and accumulate an array of organolep
As no P. alecto miRNAs were known prior to this undertaking, miRDeep2 was provided with a large set of learning information in the form of all known vertebrate miRNAs from a recent release of miRBase (version 19). This resulted in identification of 426 distinct miRNA precursors, from which...