EGASP: the human ENCODE genome annotation assessment project
Background We present the results of EGASP, a community experiment to assess the state-
of-the-art in genome annotation within the ENCODE regions, which span 1% of the human …
of-the-art in genome annotation within the ENCODE regions, which span 1% of the human …
TSEBRA: transcript selector for BRAKER
Background BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the
accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains …
accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains …
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 …
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 …
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
Background In order to improve gene prediction, extrinsic evidence on the gene structure
can be collected from various sources of information such as genome-genome comparisons …
can be collected from various sources of information such as genome-genome comparisons …
Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts
IS Druzhinina, K Chenthamara, J Zhang… - PLoS …, 2018 - journals.plos.org
Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are
aggressive parasites of other fungi and efficient decomposers of plant biomass. Although …
aggressive parasites of other fungi and efficient decomposers of plant biomass. Although …
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
M Stanke, A Tzvetkova, B Morgenstern - Genome biology, 2006 - Springer
Background A large number of gene prediction programs for the human genome exist.
These annotation tools use a variety of methods and data sources. In the recent ENCODE …
These annotation tools use a variety of methods and data sources. In the recent ENCODE …
Approaches to fungal genome annotation
Fungal genome annotation is the starting point for analysis of genome content. This
generally involves the application of diverse methods to identify features on a genome …
generally involves the application of diverse methods to identify features on a genome …
Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning
For modern biology, precise genome annotations are of prime importance, as they allow the
accurate definition of genic regions. We employ state-of-the-art machine learning methods to …
accurate definition of genic regions. We employ state-of-the-art machine learning methods to …
Reference based annotation with GeneMapper
S Chatterji, L Pachter - Genome biology, 2006 - Springer
We introduce GeneMapper, a program for transferring annotations from a well annotated
genome to other genomes. Drawing on high quality curated annotations, GeneMapper …
genome to other genomes. Drawing on high quality curated annotations, GeneMapper …