GeneID

[…] project id prjna380580. sequenced reads were mapped to the reference gene models for atlantic salmon (ncbi salmo salar annotation release 100) using bowtie233. read counts were summed for each unique geneid and normalized by total mapped read counts. statistical analysis for detection of differentially expressed genes was done using noiseqbio from the noiseq package34, with threshold of pnoi = 0.9 […]

[…] benchmark universal single-copy orthologs (buscos). 805 complete genes, 201 fragmented and 432 missing buscos were found in this draft assembled genome sequence for this strain. the gene predictor geneid (http://genome.crg.es/software/geneid/) predicted 21,876 genes using the previously sequenced plant pathogenic relative, p. infestans as a training model., primary annotation of predicted […]

[…] (buscos). 805 complete genes, 201 fragmented and 432 missing buscos were found in this draft assembled genome sequence for this strain. the gene predictor geneid (http://genome.crg.es/software/geneid/) predicted 21,876 genes using the previously sequenced plant pathogenic relative, p. infestans as a training model., primary annotation of predicted sequences revealed 9989 sequences […]

[…] dn/ds median of each atgc was determined using fisher’s exact test., integrated protein abundance levels for e. coli k12 mg1655 were downloaded from paxdb34. each protein id was mapped to its refseq geneid, for which the start codon was extracted from the whole genome sequence nc_000913.3. taking into account only genes with protein abundance above the median (3.95 ppm), the protein abundances […]

[…] build the phylogenetic tree of the periplasmic components from the abc transporters related to sulfate or sulfonates uptake found in x. citri, the gene sequences of the periplasmic proteins [ssua1 (geneid: 1154920), ssua2 (geneid: 1157269) and sbp (geneid: 1155088)] were submitted to the blastp using the non-redundant sequence database. the criterion of choice of the proteins and microorganisms […]