A hitchhiker's guide to expressed sequence tag (EST) analysis

By Shivashankar H. Nagaraj, Robin B. Gasser, Shoba Ranganathan. Briefings Bioinform., 2006

302 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/eb2b47bff5ca97655d5becab27c82b0885801050

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Citations in the corpus

Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics (2007, background): “A few relevant examples are ESTExplorer, ESTIMA, ESTree or JUICE (see [2] for a survey in EST analysis).”
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing (2008, background): “Whole genome or transcriptome sequencing enables functional genomic studies based on global gene expression, single nucleotide polymorphism (SNP) surveys, quantitative trait loci (QTL) studies, genomic scans of diversity, and so forth (Rudd 2003; Bouck & Vision 2007; Nagaraj et al. 2007).”
High-throughput functional annotation and data mining with the Blast2GO suite (2008, methodology): “Apart from the automatic GO annotation of EST collections (22–24) and the functional interpretation of Microarray studies (25–28) Blast2GO has been applied to genome comparison studies (29,30) and general bioinformatics methodology descriptions (23,24,31) over a wide range of biological taxons (Stre”
Genome-wide responses to drought in forest trees (2011, background): “Although the identification of drought-induced ESTs in forest trees was important for early gene identification and transcriptome studies, the EST libraries generated from these studies played key roles in founding broader analyses of tree transcriptome activity (Nagaraj et al., 2007).”
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine (2007, background): “Known for its error tolerance, framefinder can identify most correct ORFs even when the input transcripts contain sequencing errors such as point mutations, indels and truncations (14,15).”