GeneID pipeline

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


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Maintainer


  • person_outline Enrique Blanco <>

Publications for GeneID

GeneID IN pipelines

 (15)
2018
PMCID: 5789820
PMID: 29382956
DOI: 10.1038/s41598-018-20308-1

[…] 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 […]

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

[…] (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 […]

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 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 […]

2015
PMCID: 4501297
PMID: 26169280
DOI: 10.1186/s12864-015-1736-5

[…] 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 […]

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

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