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tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection
Initial sequencing and analysis of the human genome.
TLDR
The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
TLDR
Online implementations of tRNAscan-SE, snoscan and snoGPS are described that make these RNA detection tools accessible to a wider range of research biologists.
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
TLDR
This update of the tRNAscan-SE On-line resource ties together improvements in tRNA classification with greatly enhanced biological context via dynamically generated links between web server search results, the most relevant genes in the GtRNAdb and interactive, rich genome context provided by UCSC genome browsers.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
TLDR
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
The genome sequence of Schizosaccharomyces pombe
TLDR
The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote, is sequenced and highly conserved genes important for eukARYotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing are identified.
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
TLDR
The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 is reported, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria.
tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.
TLDR
This chapter describes the use of the UNIX command-driven and online web versions of tRNAscan-SE, illustrating different search modes and options.
Genome sequence of Halobacterium species NRC-1.
TLDR
Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms.
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
TLDR
The Genomic tRNA Database (GtRNAdb), currently including over 74 000 tRNA genes predicted from 740 species, is created, currently including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments.
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