GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs

A Comprehensive Benchmark of Tools for Efficient Genomic Interval Querying

Efficiently querying genomic intervals is fundamental to modern bioinformatics, enabling researchers to extract and analyze specific regions from large genomic datasets. While various tools have been developed for this purpose, there lacks a comprehensive comparison of their performance, memory usage, and practical utility. We present a systematic evaluation of genomic interval query tools using simulated datasets of varying sizes. Our benchmarking framework, segmeter, assesses both basic and complex interval queries, examining runtime performance, memory efficiency, and query precision across different tools and data structures. This comprehensive analysis provides insights into the strengths and limitations of different approaches to genomic interval querying, offering guidance for tool selection based on specific use cases and data requirements. The segmeter framework and all benchmark data are freely available, facilitating reproducibility and enabling researchers to conduct their own comparative analyses.

Interplay between non-coding RNA transcription, stringent phenotype and antibiotic production in Streptomyces

While in recent years the key role of non-coding RNAs (ncRNAs) in regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces, and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: i.) the wild type strain; ii.) an isogenic pirA-defective mutant with central carbon metabolism imbalance, "relaxed" phenotype, and repression of antibiotic production; iii.) a pirA-derivative strain harboring a "stringent" RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.

Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens

While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: (i) the wild-type strain; (ii) an isogenic pirA-defective mutant with central carbon metabolism imbalance, “relaxed” phenotype, and repression of antibiotic production; and (iii) a pirA-derivative strain harboring a “stringent” RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that the expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response.