The UCSC Archaeal Genome Browser: 2012 update

Discovery of permuted and recently split transfer RNAs in Archaea

(2011) Patricia P Chan et al.   GENOME BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Large-Scale tRNA Intron Transposition in the Archaeal Order Thermoproteales Represents a Novel Mechanism of Intron Gain

(2010) K. Fujishima et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex

(2009) Caryn R. Hale et al.   CELL

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The comprehensive microbial resource

(2009) Tanja Davidsen et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea

(2009) Kosuke Fujishima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional Map of Respiratory Versatility in the Hyperthermophilic CrenarchaeonPyrobaculum aerophilum

(2008) Aaron E. Cozen et al.   JOURNAL OF BACTERIOLOGY

OperonDB: a comprehensive database of predicted operons in microbial genomes

(2008) M. Pertea et al.   NUCLEIC ACIDS RESEARCH

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

MODBASE, a database of annotated comparative protein structure models and associated resources

(2008) U. Pieper et al.   NUCLEIC ACIDS RESEARCH