Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation
tool that reports eukaryotic gene structures as a weighted consensus of all available …
tool that reports eukaryotic gene structures as a weighted consensus of all available …
Computational gene prediction using multiple sources of evidence
This article describes a computational method to construct gene models by using evidence
generated from a diverse set of sources, including those typical of a genome annotation …
generated from a diverse set of sources, including those typical of a genome annotation …
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Motivation: Computational annotation of protein coding genes in genomic DNA is a widely
used and essential tool for analyzing newly sequenced genomes. However, current …
used and essential tool for analyzing newly sequenced genomes. However, current …
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes
We have developed a portable and easily configurable genome annotation pipeline called
MAKER. Its purpose is to allow investigators to independently annotate eukaryotic genomes …
MAKER. Its purpose is to allow investigators to independently annotate eukaryotic genomes …
Automatic annotation of eukaryotic genes, pseudogenes and promoters
V Solovyev, P Kosarev, I Seledsov, D Vorobyev - Genome biology, 2006 - Springer
Background The ENCODE gene prediction workshop (EGASP) has been organized to
evaluate how well state-of-the-art automatic gene finding methods are able to reproduce the …
evaluate how well state-of-the-art automatic gene finding methods are able to reproduce the …
JIGSAW: integration of multiple sources of evidence for gene prediction
JE Allen, SL Salzberg - Bioinformatics, 2005 - academic.oup.com
Motivation: Computational gene finding systems play an important role in finding new
human genes, although no systems are yet accurate enough to predict all or even most …
human genes, although no systems are yet accurate enough to predict all or even most …
Structural and functional annotation of eukaryotic genomes with GenSAS
Abstract The Genome Sequence Annotation Server (GenSAS, https://www. gensas. org) is a
secure, web-based genome annotation platform for structural and functional annotation, as …
secure, web-based genome annotation platform for structural and functional annotation, as …
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus
Motivation: Accurate gene structure annotation is a challenging computational problem in
genomics. The best results are achieved with spliced alignment of full-length cDNAs or …
genomics. The best results are achieved with spliced alignment of full-length cDNAs or …
Annotating eukaryote genomes
The Genome Annotation Assessment Project tested current methods of gene identification,
including a critical assessment of the accuracy of different methods. Two new databases …
including a critical assessment of the accuracy of different methods. Two new databases …
Genome annotation in plants and fungi: EuGene as a model platform
In this era of whole genome sequencing, reliable genome annotations (identification of
functional regions) are the cornerstones for many subsequent analyses. Not only is careful …
functional regions) are the cornerstones for many subsequent analyses. Not only is careful …