PIPE-chipSAD is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm chipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure, align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions. Finally, the pipeline includes anno-chipSAD a method to annotate the detected transcripts in comparison to the genome annotation. Overall, our pipeline allows transcriptional profile analysis of both coding and non-coding portions of the chromosome in a single framework. Importantly, due to its versatile characteristics, it will be of wide applicability to analyse, not only microarray signals, but also data from other high throughput technologies such as RNA-sequencing. The current PIPE-chipSAD implementation is written in Python programming language and is freely available at https://github.com/silviamicroarray/chipSAD.

Bottini, S.; Del Tordello, E.; Fagnocchi, L.; Donati, C.; Muzzi, A. (2016). PIPE-chipSAD: A pipeline for the analysis of high density arrays of bacterial transcriptomes. FRONTIERS IN MOLECULAR BIOSCIENCES, 3 (82): 1-7. doi: 10.3389/fmolb.2016.00082 handle: http://hdl.handle.net/10449/37563

PIPE-chipSAD: A pipeline for the analysis of high density arrays of bacterial transcriptomes

Bottini, Silvia;Donati, Claudio;
2016-01-01

Abstract

PIPE-chipSAD is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm chipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure, align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions. Finally, the pipeline includes anno-chipSAD a method to annotate the detected transcripts in comparison to the genome annotation. Overall, our pipeline allows transcriptional profile analysis of both coding and non-coding portions of the chromosome in a single framework. Importantly, due to its versatile characteristics, it will be of wide applicability to analyse, not only microarray signals, but also data from other high throughput technologies such as RNA-sequencing. The current PIPE-chipSAD implementation is written in Python programming language and is freely available at https://github.com/silviamicroarray/chipSAD.
Settore BIO/11 - BIOLOGIA MOLECOLARE
2016
Bottini, S.; Del Tordello, E.; Fagnocchi, L.; Donati, C.; Muzzi, A. (2016). PIPE-chipSAD: A pipeline for the analysis of high density arrays of bacterial transcriptomes. FRONTIERS IN MOLECULAR BIOSCIENCES, 3 (82): 1-7. doi: 10.3389/fmolb.2016.00082 handle: http://hdl.handle.net/10449/37563
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/37563
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