GeneID protocols

View GeneID computational protocol

GeneID statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Protein-coding gene prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

GeneID specifications

Information


Unique identifier OMICS_07789
Name GeneID
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA
Output data A series of genes predicted along the input sequence.
Output format GFF,XML
Operating system Unix/Linux
Computer skills Advanced
Version 1.4.4
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Enrique Blanco <>

Publications for GeneID

GeneID in pipelines

 (20)
2018
PMCID: 5796402
PMID: 29390967
DOI: 10.1186/s12859-018-2041-5

[…] 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 […]

2018
PMCID: 5796402
PMID: 29390967
DOI: 10.1186/s12859-018-2041-5

[…] 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 […]

2018
PMCID: 5852110
PMID: 29568289
DOI: 10.3389/fmicb.2018.00406

[…] (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 […]

2017
PMCID: 5435576
PMID: 28560165
DOI: 10.1016/j.gdata.2017.05.010

[…] 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 […]

2017
PMCID: 5622118
PMID: 28963504
DOI: 10.1038/s41598-017-12619-6

[…] 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 […]


To access a full list of citations, you will need to upgrade to our premium service.

GeneID in publications

 (823)
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] 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 […]

PMCID: 5944373
PMID: 29760869
DOI: 10.1080/20013078.2018.1470442

[…] 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 […]

PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] 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 […]

PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] 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 […]

PMCID: 5924555
PMID: 29659530
DOI: 10.3390/genes9040213

[…] []. 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 […]


To access a full list of publications, you will need to upgrade to our premium service.

GeneID institution(s)
Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Spain

GeneID reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GeneID