Using geneid to Identify Genes

By Enrique Blanco, Genís Parra, Roderic Guigó. Current Protocols in Bioinformatics, 2002

457 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Long non-coding RNAs with enhancer-like function in human (2010, methodology): “Analysis of protein coding potential of the ncRNAs using GeneID (Blanco et al., 2007; Parra et al., 2000) shows ncRNAs coding potential comparable to that of ancestral repeats (Lunter et al.”
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics (2017, background): “2011), GENEID (Blanco et al. 2007), GeneMark (Borodovsky and Lomsadze 2011), and SNAP (Korf 2004) need to optimize their parameter configurations for each genome in order to achieve the best results.”
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome (2017, background): “Biases in nucleotide frequencies and codon usage have already been described in the literature as important discriminative features between coding and non-coding RNAs (21,31).”
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression (2012, methodology): “To assess the protein-coding status of the present lncRNAs catalog, we first used the program GeneID (Blanco et al. 2007) to (1) measure the protein-coding potential and (2) find the longest possible ORF in each lncRNA sequence.”