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iPARS

Structural profiles of Yeast RNAs


The structural profiles of the 3083 transcripts for which an average nucleotide coverage above 1.0 was obtained can be downloaded below. The full list of these transcripts, which include 3000 yeast coding transcripts, 14 tRNAs, 5 rRNAs, and 64 other annotated non-coding genes is found in Supplementary Table 3.

Versions history

  1. PARS catalog version 1 (May-2010): Pre-publication release.
  2. PARS catalog version 2 (September-2010): Added file containing PARS-assisted folding in bracket notation

Download data


Reference transcriptomein FASTA format
Global coordinates of transcribed genesFile has 5 columns in the following format: Gene ID (column 1), Chromosome (column 2), Feature start position (column 3), Feature end position (column 4), Feature type (column 5, "Transcript" covers the entire transcript, "5UTR" and "3UTR" denote untranslated areas, "Exon" denotes coding exon and could occur more than once for a given gene in case the gene is spliced).
Local coordinates of transcribed genesFile has 4 columns in the following format: Gene ID (column 1), Feature type (column 2, "Transcript" always starts at 1 and covers the entire transcript, "5UTR" and "3UTR" annotate untranslated regions, "CDS" annotates the coding sequence), Feature start position (column 3), Feature end position (column 4).
Structural profilesFiles have 3 columns in the following format: Gene ID (column 1), Gene length (column 2), Data (column 3, semicolon separated, representing either the PARS score or the raw number of reads obtained for each base).V1 Reads

S1 Reads

Score

PARS-assisted foldingFile has 3 columns in the following format: Gene ID (column 1), sequence (column 2) and PARS-assisted folding (column 3, in bracket notation).
Overlapping PeaksList of nucleotides showing strong peaks in both V1- and S1-treated samples. File has 3 columns in the following format: Gene ID (column 1), number of peaks (column 2), genomic location in local transcript coordinates of the peaks (column 3, semicolon separated).