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Full-length transcriptome assembly from RNA-Seq data without a reference genome.
The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample. Expand
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. Expand
UCHIME improves sensitivity and speed of chimera detection
UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. Expand
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation. Expand
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to aExpand
Structure, Function and Diversity of the Healthy Human Microbiome
The Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far, finding the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. Expand
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
A new chimera detection tool called Chimera Slayer (CS), which detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets. Expand
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations. Expand
The TIGR Rice Genome Annotation Resource: improvements and new features
  • S. Ouyang, Wei Zhu, +11 authors C. Buell
  • Medicine, Computer Science
  • Nucleic Acids Res.
  • 1 December 2006
Through incorporation of multiple transcript and proteomic expression data sets, the Institute for Genomic Research has been able to annotate 24 799 genes (31 739 gene models), representing ∼50% of the total gene models, as expressed in the rice genome. Expand
The Genome of the African Trypanosome Trypanosoma brucei
Comparisons of the cytoskeleton and endocytic trafficking systems of Trypanosoma brucei with those of humans and other eukaryotic organisms reveal major differences. Expand