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Protocols

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


No version available

Maintainer


  • person_outline Enrique Blanco

Publications for GeneID

GeneID citations

 (341)
library_books

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

2018
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 […]

library_books

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

2018
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 […]

library_books

Genome Sequence of the Freshwater Yangtze Finless Porpoise

2018
Genes
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 […]

library_books

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

2018
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 […]

call_split

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

2018
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). […]

library_books

An Ontology Systems Approach on Human Brain Expression and Metaproteomics

2018
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 […]

Citations

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

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