Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation

Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

(2016) Virag Sharma et al.   NUCLEIC ACIDS RESEARCH

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

(2013) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

(2011) M. F. Lin et al.   GENOME RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Direct mapping and alignment of protein sequences onto genomic sequence

(2008) Osamu Gotoh   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY