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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
Using geneid to identify genes.
GeneID in Drosophila.
GeneID citations
(832)Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy
[…] 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 […]
Metabolic alterations in urine extracellular vesicles are associated to prostate cancer pathogenesis and progression
[…] 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 […]
De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication
[…] 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 […]
The Gastrodia elata genome provides insights into plant adaptation to heterotrophy
[…] 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 […]
Genome Sequence of the Freshwater Yangtze Finless Porpoise
[…] []. 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
[…] 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 […]
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