GeneID

[…] the annotation objects for variant “chr6:g.26093141g > a” and “chr12:g.111351981c > t”.parse the annotation objects to get the ncbi gene ids related to these variants from the dbsnp.gene.geneid field, which are “3077” and “4633”.query mygene.info to retrieve the annotation objects for ncbi gene “3077” and “4633”.parse the annotation objects to get the wikipathways [] ids related […]

[…] the annotation objects for variant “chr6:g.26093141g > a” and “chr12:g.111351981c > t”., parse the annotation objects to get the ncbi gene ids related to these variants from the dbsnp.gene.geneid field, which are “3077” and “4633”., query mygene.info to retrieve the annotation objects for ncbi gene “3077” and “4633”., parse the annotation objects to get the wikipathways [] ids related […]

[…] (see figure , data “human gene hits”). the human protein hits of the last iteration were extracted from the files and redundancies removed. each list of non-redundant proteins was annotated with its geneid by using the gcrh38 database., the human rna-seq database at the allen brain atlas contains normalized expression data on 22,318 genes. to see the normalization methods used go […]

[…] 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 […]

[…] 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 paxdb. 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 […]

[…] literature review, information from pharmgkb (http://www.pharmgkb.org/) has also been referenced. as a result, six membrane transporters implicated in the uptake of gemcitabine i.e. slc28a1 (entrez geneid:9154), slc28a2 (entrez geneid:9153), slc28a3 (entrez geneid:64078), slc29a1 (entrez geneid:2030), slc29a2 (entrez geneid:3177), slc29a3 (entrez geneid:55315) and three transporters implicated […]

[…] nucleotide accession., for each metabolite included in this step, we reported: for kegg compounds, the related enzymes ec number, uniprot accession, uniprot entry name, kegg gene id, gene symbol, geneid and the genbank nucleotide accession for the corresponding transcripts.for hmdb compounds, the hmdb enzyme gene symbol, gene symbol, gene id and genbank nucleotide accession […]

[…] al., ). reverse translation allowed us to find the genome coordinates of hnt. the complete genomic region was screened for coding-sequences (cds) using mrna prediction tools like augustus, fgenesh, geneid, genemark, and genscan (burge and karlin, ; salamov and solovyev, ; besemer and borodovsky, ; blanco et al., ; keller et al., )., the sequences of hnt and mammal orthologue ras responding […]

[…] 2.0.8) to identify putative exon regions and splice junctions; cufflinks (version 2.1.1) was then used to assemble the mapped reads into gene models (cufflinks-set). augustus (version 2.5.5), geneid (version), genescan (version 1.0), glimmerhmm (version 3.0.1), and snap (version) were also used to predict coding regions in the repeat-masked genome. of these, augustus, snap and glimmerhmm […]

[…] []. then, we used exonerate v2.2 [] to filter the genome sequences and the corresponding query proteins and search for accurately spliced alignments. for de novo annotation, augustus v3.2.1 [], geneid v1.4.4 [], and glimmerhmm v3.0.3 [] were used to predict genes within the genome on the basis of a human training set. next, we used evidencemodeler v1.1.1 [] to integrate homologs and de novo […]