Omics

Repeat Explorer of TN20

RepeatExplorer is an online tool that can give a bioinformatician a grasp on what repeats are in a genome, as well as their relative abundance.  Here, I took TN20 reads from NCBI (SRR1800548), trimmed with trimmomatic, converted to fasta with the fastx-toolkit, and sorted and interlaced with seqtk.  200,000 reads were retained that maintained the maximum length (150bp) and had a full length mate. Classified repeats were also obtained from running RepeatModeler on the H. glycines genome [1]. Read more about Repeat Explorer of TN20

Secreted Genes in the H. glycines V1 genome

Because secreted proteins play a vital role in H. glycines parasitism, iwe surveyed the H. glycines annotation for genes with a signal peptide for secretion that also lack a transmembrane domain (1).  A total of 2,222 genes were classified as secreted using Phobius (2) and SignalP (3) annotations obtained using interproscan(4).  However, due to a coding error, these annotations were incomplete.  With SignalP 4.0 (3) we have identified a larger set of secreted genes, 4,656.

  Read more about Secreted Genes in the H. glycines V1 genome

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