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MIRPIPE: quantification of microRNAs in niche model organisms
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| Zeitschriftentitel: | Bioinformatics |
|---|---|
| Personen und Körperschaften: | , , , , |
| In: | Bioinformatics, 30, 2014, 23, S. 3412-3413 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Kuenne, Carsten Preussner, Jens Herzog, Mario Braun, Thomas Looso, Mario Kuenne, Carsten Preussner, Jens Herzog, Mario Braun, Thomas Looso, Mario |
|---|---|
| author |
Kuenne, Carsten Preussner, Jens Herzog, Mario Braun, Thomas Looso, Mario |
| spellingShingle |
Kuenne, Carsten Preussner, Jens Herzog, Mario Braun, Thomas Looso, Mario Bioinformatics MIRPIPE: quantification of microRNAs in niche model organisms Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
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kuenne, carsten |
| spelling |
Kuenne, Carsten Preussner, Jens Herzog, Mario Braun, Thomas Looso, Mario 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btu573 <jats:title>Abstract</jats:title> <jats:p>Summary: MicroRNAs (miRNAs) represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such tools. Here we introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public- or user-uploaded reference databases.</jats:p> <jats:p>Availability and implementation: The Web service is freely available at http://bioinformatics.mpi-bn.mpg.de. MIRPIPE was implemented in Perl and integrated into Galaxy. An offline version for local execution is also available from our Web site.</jats:p> <jats:p>Contact: Mario.Looso@mpi-bn.mpg.de</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> MIRPIPE: quantification of microRNAs in niche model organisms Bioinformatics |
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10.1093/bioinformatics/btu573 |
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Oxford University Press (OUP), 2014 |
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MIRPIPE: quantification of microRNAs in niche model organisms |
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MIRPIPE: quantification of microRNAs in niche model organisms |
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MIRPIPE: quantification of microRNAs in niche model organisms |
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MIRPIPE: quantification of microRNAs in niche model organisms |
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MIRPIPE: quantification of microRNAs in niche model organisms |
| title_short |
MIRPIPE: quantification of microRNAs in niche model organisms |
| title_sort |
mirpipe: quantification of micrornas in niche model organisms |
| topic |
Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| url |
http://dx.doi.org/10.1093/bioinformatics/btu573 |
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2014 |
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3412-3413 |
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<jats:title>Abstract</jats:title>
<jats:p>Summary: MicroRNAs (miRNAs) represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such tools. Here we introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public- or user-uploaded reference databases.</jats:p>
<jats:p>Availability and implementation: The Web service is freely available at http://bioinformatics.mpi-bn.mpg.de. MIRPIPE was implemented in Perl and integrated into Galaxy. An offline version for local execution is also available from our Web site.</jats:p>
<jats:p>Contact: Mario.Looso@mpi-bn.mpg.de</jats:p>
<jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> |
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| description | <jats:title>Abstract</jats:title> <jats:p>Summary: MicroRNAs (miRNAs) represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such tools. Here we introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public- or user-uploaded reference databases.</jats:p> <jats:p>Availability and implementation: The Web service is freely available at http://bioinformatics.mpi-bn.mpg.de. MIRPIPE was implemented in Perl and integrated into Galaxy. An offline version for local execution is also available from our Web site.</jats:p> <jats:p>Contact: Mario.Looso@mpi-bn.mpg.de</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> |
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| spelling | Kuenne, Carsten Preussner, Jens Herzog, Mario Braun, Thomas Looso, Mario 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btu573 <jats:title>Abstract</jats:title> <jats:p>Summary: MicroRNAs (miRNAs) represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such tools. Here we introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public- or user-uploaded reference databases.</jats:p> <jats:p>Availability and implementation: The Web service is freely available at http://bioinformatics.mpi-bn.mpg.de. MIRPIPE was implemented in Perl and integrated into Galaxy. An offline version for local execution is also available from our Web site.</jats:p> <jats:p>Contact: Mario.Looso@mpi-bn.mpg.de</jats:p> <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p> MIRPIPE: quantification of microRNAs in niche model organisms Bioinformatics |
| spellingShingle | Kuenne, Carsten, Preussner, Jens, Herzog, Mario, Braun, Thomas, Looso, Mario, Bioinformatics, MIRPIPE: quantification of microRNAs in niche model organisms, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| title | MIRPIPE: quantification of microRNAs in niche model organisms |
| title_full | MIRPIPE: quantification of microRNAs in niche model organisms |
| title_fullStr | MIRPIPE: quantification of microRNAs in niche model organisms |
| title_full_unstemmed | MIRPIPE: quantification of microRNAs in niche model organisms |
| title_short | MIRPIPE: quantification of microRNAs in niche model organisms |
| title_sort | mirpipe: quantification of micrornas in niche model organisms |
| title_unstemmed | MIRPIPE: quantification of microRNAs in niche model organisms |
| topic | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| url | http://dx.doi.org/10.1093/bioinformatics/btu573 |