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Chimira: analysis of small RNA sequencing data and microRNA modifications.

Vitsios DM, Enright AJ - Bioinformatics (2015)

Bottom Line: Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material).A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material.Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

No MeSH data available.


Modification profile from 12 Heart, Liver and Brain tissue samples in H. sapiens, as detected by Chimira: (a) Global profile (b) 3′-Modifications (c) 5′-Modifications (d) Internal modifications (ADAR edits and SNPs) (e) Internal modifications (SNPs). The x-axis corresponds to the index positions across a miRNA molecule. They y-axis corresponds to the raw counts of the identified modification patterns. The start of a miRNA on the x-axis is at index ‘0’ (5′ end) while its end is at index ‘22’ (3′ end)
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btv380-F1: Modification profile from 12 Heart, Liver and Brain tissue samples in H. sapiens, as detected by Chimira: (a) Global profile (b) 3′-Modifications (c) 5′-Modifications (d) Internal modifications (ADAR edits and SNPs) (e) Internal modifications (SNPs). The x-axis corresponds to the index positions across a miRNA molecule. They y-axis corresponds to the raw counts of the identified modification patterns. The start of a miRNA on the x-axis is at index ‘0’ (5′ end) while its end is at index ‘22’ (3′ end)

Mentions: Secondly, ‘modifications’ refers to the quantification of any sequence segments that are part of the input sequences and cannot be explained by genomic sequence. In the example shown (Fig. 1), uridylation and adenylation are the most prevalent modification types in the 1 nt after the 3′ end of the miRNAs, while C modifications are highly enriched exactly at the 3′ end. ADAR editing is the predominant modification type in the internal modifications followed by a moderately expressed C-SNP, 11 nt upstream of the 3′ end (index position: 11).Fig. 1.


Chimira: analysis of small RNA sequencing data and microRNA modifications.

Vitsios DM, Enright AJ - Bioinformatics (2015)

Modification profile from 12 Heart, Liver and Brain tissue samples in H. sapiens, as detected by Chimira: (a) Global profile (b) 3′-Modifications (c) 5′-Modifications (d) Internal modifications (ADAR edits and SNPs) (e) Internal modifications (SNPs). The x-axis corresponds to the index positions across a miRNA molecule. They y-axis corresponds to the raw counts of the identified modification patterns. The start of a miRNA on the x-axis is at index ‘0’ (5′ end) while its end is at index ‘22’ (3′ end)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4595902&req=5

btv380-F1: Modification profile from 12 Heart, Liver and Brain tissue samples in H. sapiens, as detected by Chimira: (a) Global profile (b) 3′-Modifications (c) 5′-Modifications (d) Internal modifications (ADAR edits and SNPs) (e) Internal modifications (SNPs). The x-axis corresponds to the index positions across a miRNA molecule. They y-axis corresponds to the raw counts of the identified modification patterns. The start of a miRNA on the x-axis is at index ‘0’ (5′ end) while its end is at index ‘22’ (3′ end)
Mentions: Secondly, ‘modifications’ refers to the quantification of any sequence segments that are part of the input sequences and cannot be explained by genomic sequence. In the example shown (Fig. 1), uridylation and adenylation are the most prevalent modification types in the 1 nt after the 3′ end of the miRNAs, while C modifications are highly enriched exactly at the 3′ end. ADAR editing is the predominant modification type in the internal modifications followed by a moderately expressed C-SNP, 11 nt upstream of the 3′ end (index position: 11).Fig. 1.

Bottom Line: Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material).A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material.Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

No MeSH data available.