Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and evolution of spliceosomal introns

(2012) Igor B Rogozin et al.   Biology Direct

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

(2012) Hiroaki Iwata et al.   NUCLEIC ACIDS RESEARCH

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Comparative analysis of information contents relevant to recognition of introns in many species

(2011) Hiroaki Iwata et al.   BMC GENOMICS

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

(2011) Johannes Söding et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

WormBase 2012: more genomes, more data, new website

(2011) K. Yook et al.   NUCLEIC ACIDS RESEARCH

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence-based gene predictions in plant genomes

(2009) C. Liang et al.   GENOME RESEARCH

The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes

(2009) James C Estill et al.   Plant Methods

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Identifying protein-coding genes in genomic sequences

(2009) Jennifer Harrow et al.   GENOME BIOLOGY

Direct mapping and alignment of protein sequences onto genomic sequence

(2008) Osamu Gotoh   BIOINFORMATICS

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

(2008) Alinda Nagy et al.   BMC BIOINFORMATICS

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence

(2008) Osamu Gotoh   NUCLEIC ACIDS RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY