================================================== Benchmark set for bacterial sRNA target predictors Supplementary files ================================================== Adrien Pain, Daniel Gautheret Universite Paris Sud July 30, 2014 File description ================ TableS1-trusted-pairs.xlsx (Table S1) -------------------------------------------------- List of trusted (experimentally validated) sRNA/target pairs used as benchmark. Includes coordinates of published interactions, references and evidence level. NC_000913_CDS_-200nt_100nt.fa ----------------------------- 5' regions of E. coli K12 genes obtained by automatic extraction of -200/+100 fragments around each start codon (4317 regions). Strain: Escherichia coli str. K-12 substr. MG1655. Coordinates are given for assembly #2: NC_000913.2 NC_000913_RNA-seq_TSS.fa -------------------------- 5' regions of E. coli K12 genes extracted based on actual RNAseq-derived TSS (1). For each TSS in Table S5 and S9 of Li et al.'s paper (1), we extracted the region from the TSS to 100 nt past the start codon. For genes not expressed in the RNAseq data or genes preceeded by other genes in an operon, we extracted the -200/+100 region around ATG as above. (total: 4317 regions) Strain: Escherichia coli str. K-12 substr. MG1655 coli_sRNA_vx.fa ---------------- All coli sRNA sequences to be used for target prediction. coli_targetpairs_Vx.tsv coli_targetpairs_Vx_direct.tsv ------------------------------- Flat file extracts from table of true target pairs, for programmatic usage. The "direct" version includes only those pairs supported by direct experimental evidence. The "direct" version includes only those pairs supported by direct experimental evidence. coli_pairs_Vx_with_compMut_realUTR.tsv coli_pairs_Vx_with_compMut_defaultUTR.tsv ----------------------------------------- Files containing the list of base pairs with experimental compensatory mutation support (same references as in coli_targetpairs above). Relative coordinates of each individual base pair are provided, in the order: sRNA position, base, mRNA position, base. As mRNA coordinates differ when using real or default (-200/+100) UTRs, a specific file is provided for each system. IstR.fa, RseX.fa, RydC.fa --------------------------- Set of homologous sequences for sRNAs not available in the copraRNA server. command-lines.txt ------------------ Text file containing all Unix command lines and options used for running predictors. Also includes authors and program versions. References: =========== (1) Li S et al. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics 2013, 14:520.