In order to create input for functional analyses, the blastx (nucleotide-to-protein) program was run on all the filtered contigs on the TimeLogic DeCypher boards, against the “nr” database with 81,622,391 protein sequences downloaded from NCBI on February 12, 2016. The blastn results ...
For example, the Cetobacterium ASV, which showed the strongest positive partial correlation with eels’ activity level, was represented by the 16S rRNA sequences completely matching that of Cetobacterium somerae (formerly recognized as “Bacteroides type A”) in the NCBI nucleotide database. This ...
degenerate oligo= oligo nucleotide sequence with degeneracies Example:ATACGTAY expanded oligo= all non-degenerate sequences encoded by the degenerate sequence Example:ATACGTAY=(ATACGTAC, ATACGTAT) Description $OUTDIR/core_clusters_info.tsv General metadata on all core gene clusters ...
Individuals with ambiguous nucleotide calls were excluded from analysis. Phenotypic data were categorized based on the identified haplotypes and used to test for association. One way ANOVA with Duncan's test as a post hoc test was used to identify significant associations and measure specific differenc...
GenBank database (accession number: NC_007089.4) was used as an outgroup for these phylogenetic analyses. Overall, the identification ofAcanthamoebaspecies was based on the two following criteria: nucleotide similarity <100% in pairwise comparisons and bootstrap threeshold <90% in phylogenetic ...
Impairment of insulin action and metabolic dysregulation have traditionally been associated with schizophrenia, although the molecular basis of such association remains still elusive. The present meta-analysis aims to assess the impact of insulin action
Controlled degradation of proteins is necessary for ensuring their abundance and sustaining a healthy and accurately functioning proteome. One of the degradation routes involves the uncapped 20S proteasome, which cleaves proteins with a partially unfolde
(MLSA) that was applied to housekeeping genes:acnA,dnaX,gyrA,gyrBandmtlD. The initial step of the pipeline is the individual alignment of protein sequences of the five genes. Start and end gaps in the alignment were used to trim the original nucleotide sequence. A single contiguous sequence ...
These a more detailed comparison of the sequences at the results are consistent with the previous studies nucleotide level. Briefly, the statistical tools that we carried out on anaerobic digesters (Godon et al., used were efficient in showing the shared phylo- 1997a, b; Chouari et al., ...
Nucleotide sequence phylogeny for thaumarchaeal 16S rRNA (with references from NCBI nr and SILVA 138.1 Ref NR databases) and amino acid sequence phylogenies for AmoA amino acid phylogenetic trees were created as follows: Sequences were aligned using MUSCLE with default parameters [107] and trimmed ...