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Citations per year

Number of citations per year for the bioinformatics software tool GeneID

Tool usage distribution map

This map represents all the scientific publications referring to GeneID per scientific context
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GeneID specifications


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


No version available


  • person_outline Enrique Blanco

Publications for GeneID

GeneID citations


De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication

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

[…] map detailing the protein architecture is shown in Supplementary Figure .An exon prediction analysis was made using five different tools: Augustus (Keller et al., ), FGenesh (Salamov and Solovyev, ), GeneID (Blanco et al., ), GeneMark (Besemer and Borodovsky, ) and GenScan (Burge and Karlin, ). Hnt CDS and mRNA coding regions were deduced and oligonucleotide primers for hnt amplification were desi […]


The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

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

[…] els. Gene models generated from all the methods were integrated by EvidenceModeler (EVM). Weights for each type of evidence were set as follows: PASA-T-set > Homology-set > Cufflinks-set > Augustus > GeneID = SNAP = GlimmerHMM = GeneScan. The gene models were further updated by PASA2 to generate UTRs, alternative splicing variation information, which generated 26,872 gene models. Gene models only […]


Genome Sequence of the Freshwater Yangtze Finless Porpoise

PMCID: 5924555
PMID: 29659530
DOI: 10.3390/genes9040213

[…] LASTN []. 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 […]


TGFβ signaling related genes are involved in hormonal mediation during termite soldier differentiation

PLoS Genet
PMCID: 5912798
PMID: 29641521
DOI: 10.1371/journal.pgen.1007338

[…] sed as endogenous controls for constitutive expression: EF1-alfa (DDBJ/EMBL/GenBank Accession No. AB915828), beta-actin (No. AB915826), NADH-dh (No. AB936819) and three ribosomal protein genes (RS49: GeneID: KDR21989, RPS18: KDR22651 and RPL13a: KDR22610) [,]. The most appropriate gene was evaluated using GeNorm [] and NormFinder [], and EF1-alfa was selected in all real-time qPCR analyses perform […]


Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma

BMC Syst Biol
PMCID: 5883534
PMID: 29615030
DOI: 10.1186/s12918-018-0554-1
call_split See protocol

[…] ousekeeping genes like actin beta (ACTB, Gene ID: 60), cyclophilin A (PPIA, peptidylprolyl isomerase A, Gene ID: 5478) and RNA polymerase II subunit A (POLR2A, GeneID: 5430). […]


An Ontology Systems Approach on Human Brain Expression and Metaproteomics

Front Microbiol
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 to documentation a […]

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

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