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

Taxon


  • Animals
  • Fungi
  • Plants
  • Protists

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Versioning


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Maintainer


  • person_outline Enrique Blanco <>

GeneID articles

GeneID citations

 (7)
2018
PMCID: 5789820

[…] 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: 5622118

[…] 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 […]

2014
PMCID: 4035326

[…] within the contig and are scored according to the markov model in each of the possible reading frames using the transdecoder supplement of the trinity software [35], which is largely based on the geneid software [37] to remove contigs with internal stop codons and unlikely genuine coding sequences (fig. 1). after orf filtering (∼36% reduction in contigs), the 51,857 potential transcripts […]

2013
PMCID: 3706372

[…] overlapping primers (capable of amplifying both clca2 and clca4l, table s3) spanning the whole clca mrna. pcr products were purified, sequenced and aligned against clca2 (geneid: 362052) and clca4l (geneid: 499721) using “genious basic 3.7.1″ software geneious v5.3 (www.geneious.com) or clustalw (www.ebi.ac.uk/tools/msa/clustalw2)., osn-derived cilia protein extracts were performed as previously […]

2011
PMCID: 3189941

[…] srx022878. the assembled sequences have been deposited in the ncbi's transcriptome shotgun assembly (tsa) database under the accession number of hp643344 to hp701084 and can be searched using the geneid listed in additional file 1., we used the bidirectional best hit method in megablast to identify genes that are putatively orthologs between meam1 and med. pairs of sequences […]

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

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