Unfortunately, most polymorphic peptides are absent from these databases and tandem MS spectra from unlisted polymorphic peptides will inevitably remain unassigned or misassigned. We reasoned that the most straightforward solution to this conundrum would be to use next-generation sequencing data to ...
BCLAF1, a transcription regulator involved in DNA damage response20which also displayed a strong TSG score, was found to occur predominantly subclonal. Based on the union set of previously identified breast cancer drivers8,21and those identified here...
The remaining unassigned prophage, BryP1 belonged to a lineage which appears to be more closely related to Flavobacterium and Cellulophaga phages (Fig. 5). Characterisation of the three main Treponema prophage clusters The 24 prophage sequences which formed the three clear primary Treponema prophage...
When the three dwarf/small breeds were considered together, a signature of selection in the OCU2 region that harbors the LCORL and NCAPG genes was again observed, in addition to regions on several other chromosomes (OCU1, 12, 14 and 18) and unassigned scaffolds (Un0030, Un0044 and Un0076...
(TMBs) of the four mutational signatures; the results showed that SBS30, which represents DNA-based excision repair, had the highest level of TMB (Fig.1H). In addition, SBS13, representing the activity of APOBEC, was associated with the worst prognosis (Fig.1I). For comparison, the same...
Total DNA was extracted from each sample and sequenced after quality control as described in the corresponding references [15,34,104,105]. The sequences were assembled and binned with different protocols based on the batch of the samples [34,105]. In total, 495 MAGs with completeness greater ...
Since chrUn only contains unassigned sequence contigs, it was not included due to the lack of sequence and SNPs as well as the SNP mapping uncertainty. Within the placed autosomes, a total of 3,666 CNVs in 521 samples were detected and an average of 7.09 gain or loss events were evident ...
Peptide match was set to ‘Preferred’, exclude isotopes was set to ‘on’, and charge state screening was enabled to reject unassigned 1+, 7+, 8+, and > 8+ ions with a dynamic exclusion time of 20 s to discriminate against previously analyzed ions. LC-MS/MS for TMT Phosphoproteome ...
NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions,
(b) are represented in purple. Unassigned subpopulations (in orange) are low-frequency variants that we cannot assign to any of the two genotypes and shared fixed variants (in green) are common to both genotypes. C caseum, I inner wall, E external wall, H healthy tissue, N nodule, S ...