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Predicting Riboswitch Regulation on a Genomic ScaleThis page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder.InstallationCode LibrarieslibGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions for your system.Perl ModulesSeveral additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence if you have administrator privileges:
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.
BioPerlAs of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you may need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly.Riboswitch Perl ScriptsDownload the riboswitch Perl scripts.
UsageEach Perl script has POD documentation. To view it, either open the script in a text editor or use one of these commands:
Questions, comments, or problems with this procedure? Send feedback
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Added: | ||||||||
> > |
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Predicting Riboswitch Regulation on a Genomic Scale | ||||||||
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< < | This page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder. | |||||||
> > | This page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder. | |||||||
InstallationCode LibrarieslibGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions for your system.Perl ModulesSeveral additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence if you have administrator privileges:
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.
BioPerlAs of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you may need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly.Riboswitch Perl ScriptsDownload the riboswitch Perl scripts.
UsageEach Perl script has POD documentation. To view it, either open the script in a text editor or use one of these commands:
Questions, comments, or problems with this procedure? Send feedback
|
Predicting Riboswitch Regulation on a Genomic ScaleThis page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder.InstallationCode LibrarieslibGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions for your system.Perl ModulesSeveral additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence if you have administrator privileges:
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.
BioPerlAs of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you may need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly.Riboswitch Perl ScriptsDownload the riboswitch Perl scripts.
Usage | ||||||||
Changed: | ||||||||
< < | Each Perl script has POD documentation. Either open the script a text editor to view it or use one of these commands: | |||||||
> > | Each Perl script has POD documentation. To view it, either open the script in a text editor or use one of these commands: | |||||||
Questions, comments, or problems with this procedure? Send feedback
|
| ||||||||
Changed: | ||||||||
< < | Predicting Riboswitch Regulation on a Genomic Scale | |||||||
> > | Predicting Riboswitch Regulation on a Genomic Scale | |||||||
This page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder. | ||||||||
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< < | Installation | |||||||
> > | Installation | |||||||
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< < | Code Libraries | |||||||
> > | Code Libraries | |||||||
libGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions for your system. | ||||||||
Changed: | ||||||||
< < | Perl Modules | |||||||
> > | Perl Modules | |||||||
Several additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence if you have administrator privileges:
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN. | ||||||||
Changed: | ||||||||
< < | BioPerl | |||||||
> > | BioPerl | |||||||
As of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you may need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly. | ||||||||
Changed: | ||||||||
< < | Riboswitch Perl Scripts | |||||||
> > | Riboswitch Perl Scripts | |||||||
Download the riboswitch Perl scripts.
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< < | Usage | |||||||
> > | Usage | |||||||
Each Perl script has POD documentation. Either open the script a text editor to view it or use one of these commands:
Questions, comments, or problems with this procedure? Send feedback
|
Predicting Riboswitch Regulation on a Genomic ScaleThis page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder.InstallationCode LibrarieslibGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions for your system.Perl ModulesSeveral additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence if you have administrator privileges:
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.
BioPerl | ||||||||
Changed: | ||||||||
< < | As of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you will need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly. | |||||||
> > | As of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you may need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly. | |||||||
Riboswitch Perl ScriptsDownload the riboswitch Perl scripts.
UsageEach Perl script has POD documentation. Either open the script a text editor to view it or use one of these commands:
Questions, comments, or problems with this procedure? Send feedback
|
Predicting Riboswitch Regulation on a Genomic ScaleThis page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder.InstallationCode Libraries | ||||||||
Changed: | ||||||||
< < | libGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions on your system. | |||||||
> > | libGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions for your system. | |||||||
Perl Modules | ||||||||
Changed: | ||||||||
< < | Several additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence: | |||||||
> > | Several additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence if you have administrator privileges: | |||||||
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.
BioPerlAs of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you will need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly.Riboswitch Perl ScriptsDownload the riboswitch Perl scripts.
UsageEach Perl script has POD documentation. Either open the script a text editor to view it or use one of these commands:
Questions, comments, or problems with this procedure? Send feedback
|
Predicting Riboswitch Regulation on a Genomic ScaleThis page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder.InstallationCode LibrarieslibGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions on your system.Perl ModulesSeveral additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence:
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.
BioPerlAs of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you will need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly.Riboswitch Perl ScriptsDownload the riboswitch Perl scripts.
Usage | ||||||||
Changed: | ||||||||
< < | Each Perl script has POD documentation. Either open the script a text editor to view it or use one of these commands perldoc command: | |||||||
> > | Each Perl script has POD documentation. Either open the script a text editor to view it or use one of these commands: | |||||||
Questions, comments, or problems with this procedure? Send feedback
|
| ||||||||
Deleted: | ||||||||
< < | Note: This supplement / protocol is still under construction. | |||||||
Predicting Riboswitch Regulation on a Genomic ScaleThis page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder.InstallationCode Libraries | ||||||||
Changed: | ||||||||
< < | libGD is required to produce drawings of the the genomic contexts of putative RNA structure matches. Download and install according to the directions on your system. | |||||||
> > | libGD is required to produce drawings of the genomic contexts of putative RNA structure matches. Download and install according to the directions on your system. | |||||||
Perl ModulesSeveral additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence:
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.
BioPerl | ||||||||
Changed: | ||||||||
< < | As of December 2007, neither the stable or development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you will need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly. | |||||||
> > | As of December 2007, neither the stable nor development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you will need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly. | |||||||
Riboswitch Perl ScriptsDownload the riboswitch Perl scripts. | ||||||||
Changed: | ||||||||
< < |
| |||||||
> > |
| |||||||
Usage | ||||||||
Changed: | ||||||||
< < | Each Perl script has POD documentation. Either open the script a text editor to view it or use the perldoc command:
| |||||||
> > | Each Perl script has POD documentation. Either open the script a text editor to view it or use one of these commands perldoc command:
| |||||||
Questions, comments, or problems with this procedure? Send feedback | ||||||||
Added: | ||||||||
> > |
| |||||||
| ||||||||
Added: | ||||||||
> > | ||||||||
Note: This supplement / protocol is still under construction. | ||||||||
Added: | ||||||||
> > |
Predicting Riboswitch Regulation on a Genomic ScaleThis page describes how to install a set of Perl scripts designed to identify members of known riboswitch classes in genomic sequences. It accompanies a Methods in Molecular Biology protocol chapter that explains how to use these scripts. This protocol may also be useful for analyzing other structured RNAs, such as those found in the Rfam database, or for investigating new regulatory RNA motifs, such as might be predicted by CMfinder.InstallationCode LibrarieslibGD is required to produce drawings of the the genomic contexts of putative RNA structure matches. Download and install according to the directions on your system.Perl ModulesSeveral additional Perl modules from are required for the riboswitch perl scripts. You can download and install them directly from CPAN. Alternately, on MacOS X, you can use the following command sequence:
The GD module requires libGD to be installed and is only necessary for producing genomic context drawings. If you encounter any other messages of the form: "Can't locate module.pm in @INC", try installing module from CPAN.
BioPerlAs of December 2007, neither the stable or development releases of BioPerl (1.4.0 or 1.5.2) includes the necessary modules for parsing Infernal search results or manipulating Stockholm alignments. Therefore, you will need to download and install the current CVS version of bioperl-live. Either follow the Getting BioPerl instructions or try this link to download directly.Riboswitch Perl ScriptsDownload the riboswitch Perl scripts.
UsageEach Perl script has POD documentation. Either open the script a text editor to view it or use theperldoc command:
Questions, comments, or problems with this procedure? Send feedback | |||||||
Note: This supplement / protocol is still under construction. |