Jan

1

G-Mo.R-Se – build de novo gene models with RNA-Seq short reads

Filed Under Transcriptome Assembly Tools | Leave a Comment

Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models.
First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models.

G-Mo.R-Se is available at: http://www.genoscope.cns.fr/externe/gmorse/

Denoeud F, Aury JM, Da Silva C, Noel B, Rogier O, Delledonne M, Morgante M, Valle G, Wincker P, Scarpelli C, Jaillon O, Artiguenave F.  (2008) Annotating genomes with massive-scale RNA sequencing. Genome Biol. 9(12), R175. [abstract]

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  • g-mo r-se gene modeiing using rna-seq

Jan

1

MPSCAN: Fast Localisation of Multiple Reads in Genomes

Filed Under Unspliced Mapping Tools | Leave a Comment

With Next Generation Sequencers, sequence based transcriptomic or epigenomic assays yield millions of short sequence reads that need to be mapped back on a reference genome. The upcoming versions of these sequencers promise even higher sequencing capacities; this may turn the read mapping task into a bottleneck for which alternative pattern matching approaches must be experimented. Read more

Incoming search terms:

  • mpscan
  • rna seq fast analysis

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