Mutation Mapper 2.3

v2.3 Changes

This release provides a few new features:

• Genomic coordinates can be used to identify mutation consequences
• Mutation position and consequences are reported for non-coding transcripts
• Allele frequencies are reported for colocated variants
• Results are displayed with the most recent run at the top by default (configurable in the menu).

For more information see the help documentation.

INSTALL

64 bit systems only

Linux: Download the MutationMapper-2.3-1.Linux_x86_64.rpm (for RPM-based distros - e.g. CentOS), or MutationMapper-Linux_x86_64-v2.3.deb (for DEB based distros, e.g. Ubuntu) depending on your system and install via your package manager (e.g. sudo dpkg -i MutationMapper-Linux_x86_64-v2.3.deb) or, if your distribution supports it, by double-clicking the downloaded package. For Arch Linux users you may either download the prebuilt package to install via pacman (MutationMapper-Linux_x86_64-v2.3-1-x86_64.pkg.tar.xz) or the tarball (MutationMapper-2.3-1-x86_64_ArchLinux_x64.tar.gz) containing the PKGBUILD and install script.

Mac OS X: Download the MutationMapper-MacOSX-2.3.dmg disk image. Double click to open the downloaded file and drag the MutationMapper application into your Applications folder where it can be opened by double clicking. On recent versions of Mac OS X you will need to access the 'Security & Privacy' settings in System Preferences to allow this app to be opened.

Windows: Download the MutationMapper-2.3-windows-installer.exe installer application. Double click the downloaded file and follow the instructions to install. This will also launch MutationMapper once installed. To launch in future it should be accessible from the Start menu->All Programs->MutationMapper. MutationMapper will be installed to C:\Users[Your Username]\AppData\Local\MutationMapper\MutationMapper.exe.

UNINSTALL

Linux: Uninstall via your package manager (e.g. sudo apt-get remove MutationMapper).

Mac OS X: Drag the MutationMapper application from your Applications folder to the recycle bin.

Windows: MutationMapper should be installed to 'C:\Users[Your Username]\AppData\Local\MutationMapper\MutationMapper.exe'. To uninstall double-click the 'unins000.exe' file in this location. You can also access this location by right-clicking the MutationMapper application from the Start menu, selecting 'Properties' and clicking the 'Open File Location' button in the resulting window.

JAR FILE

To use the jar file download the MutationMapper_v2.3_jar.zip file and unzip. The jar can be run as normal (e.g. java -jar MutationMapper.jar) as long as it remains in the same folder as the enclosed 'lib' directory. Java version 1.8.0_51 or higher is required.

Mutation Mapper v2.2

v2.2 Changes

This release fixes various issues from v2.1:

• Fixes an issue where Ensembl REST queries would return inconsistent formatted results leading to the "java.lang.Long cannot be cast to java.lang.String" error.
• Fixes an issue where GRCh37 result links would still link to the GRCh38 site.
• Addresses an issue where flybase IDs might not be recognised.
• Fixes a problem where copying from a results table with hidden cells would lead to incorrect data being copied.
• Genomic coordinates are now reported for the site of the 'Ref' allele of a mutation instead of the full matching sequence input.
• Resized some error dialogs.

Application Info

All versions only work with 64-bit systems.

Using short sequences of wild type vs mutant DNA, MutationMapper will report the functional consequence of a given mutation, whether SNV:

...insertion:

...or deletion:

It can also be used for mapping sequences or CDS coordinates to genomic positions:

and to get mutation consequences from CDS nomenclature:

Results are reported in a detailed table, with annotations including the HGVS nomenclature, genomic position, overlap with any known variation in public databases and polyphen and SIFT predictions.

Results can be filtered to only show canonical, coding or RefSeq transcripts. The image below shows the results of four runs filtered to only show information from canonical transcripts:

For more information see the help documentation.

INSTALL

64 bit systems only

Linux: Download the MutationMapper-Linux64-2.2-1.x86_64.rpm (for RPM-based distros - e.g. CentOS), or MutationMapper-Linux64-2.2.deb (for DEB based distros, e.g. Ubuntu) depending on your system and install via your package manager (e.g. sudo dpkg -i MutationMapper-Linux64-2.2.deb) or, if your distribution supports it, by double-clicking the downloaded package. For Arch Linux users you may either download the prebuilt package to install via pacman (MutationMapper-Linux64-2.1-1.pkg.tar.xz) or the tarball (MutationMapper-2.2-1-x86_64_ArchLinux_x64.tar.gz) containing the PKGBUILD and install script.

Mac OS X: Download the MutationMapper-MacOSX-2.2.dmg disk image. Double click to open the downloaded file and drag the MutationMapper application into your Applications folder where it can be opened by double clicking. On recent versions of Mac OS X you will need to access the 'Security & Privacy' settings in System Preferences to allow this app to be opened.

Windows: _If you have a previous version of MutationMapper installed you need to uninstall it first as below._ Download the MutationMapper-2.2-windows-installer.exe installer application. Double click the downloaded file and follow the instructions to install. This will also launch MutationMapper once installed. To launch in future it should be accessible from the Start menu->All Programs->MutationMapper. MutationMapper will be installed to C:\Users[Your Username]\AppData\Local\MutationMapper\MutationMapper.exe.

UNINSTALL

Linux: Uninstall via your package manager (e.g. sudo apt-get remove MutationMapper).

Mac OS X: Drag the MutationMapperapplication from your Applications folder to the recycle bin.

Windows 7: MutationMapper should be installed to 'C:\Users[Your Username]\AppData\Local\MutationMapper\MutationMapper.exe'. To uninstall double-click the 'unins000.exe' file in this location. You can also access this location by right-clicking the MutationMapper application from the Start menu, selecting 'Properties' and clicking the 'Open File Location' button in the resulting window.

JAR FILE

To use the jar file download the MutationMapper_v2.2_jar.zip file and unzip. The jar can be run as normal (e.g. java -jar MutationMapper.jar) as long as it remains in the same folder as the enclosed 'lib' directory. Java version 1.8.0_51 or higher is required.

MutationMapper v2.1

v2.1 Changes

This release fixes some issues from v2.0 and adds some new features:

• Species choice box is now navigable with the keyboard
• Copying of hyperlinks in result table now copies the text only without the preceding junk
• Fixes an issue on Windows and Linux where some error and information dialogs would not show
• Fixed non-functioning 'Help' menu in the result window
• Fixed errors connecting to databases for some species (e.g. C. elegans and zebrafinch among others).
• Supports WormBase gene IDs
• Supports FlyBase gene and transcript IDs
• added a .jar bundle for other platforms - note that java version 1.8 is required and must be javafx enabled

Application Info

All versions only work with 64-bit systems.

Using short sequences of wild type vs mutant DNA, MutationMapper will report the functional consequence of a given mutation, whether SNV:

...insertion:

...or deletion:

It can also be used for mapping sequences or CDS coordinates to genomic positions:

and to get mutation consequences from CDS nomenclature:

Results are reported in a detailed table, with annotations including the HGVS nomenclature, genomic position, overlap with any known variation in public databases and polyphen and SIFT predictions.

Results can be filtered to only show canonical, coding or RefSeq transcripts. The image below shows the results of four runs filtered to only show information from canonical transcripts:

For more information see the help documentation.

INSTALL

64 bit systems only

Linux: Download the MutationMapper-Linux64-2.1-1.x86_64.rpm (for RPM-based distros - e.g. CentOS), MutationMapper-Linux64-2.1.deb (for DEB based distros, e.g. Ubuntu) or MutationMapper-Linux64-2.1-1.pkg.tar.xz (Arch Linux) depending on your system and install via your package manager (e.g. sudo dpkg -i MutationMapper-Linux64-2.1.deb) or, if your distribution supports it, by double-clicking the downloaded package.

Mac OS X: Download the MutationMapper-MacOSX-2.1.dmg disk image. Double click to open the downloaded file and drag the MutationMapper application into your Applications folder where it can be opened by double clicking. On recent versions of Mac OS X you will need to access the 'Security & Privacy' settings in System Preferences to allow this app to be opened.

Windows: _If you have a previous version of MutationMapper installed you need to uninstall it first as below._ Download the MutationMapper-2.1-windows-installer.exe installer application. Double click the downloaded file and follow the instructions to install. This will also launch MutationMapper once installed. To launch in future it should be accessible from the Start menu->All Programs->MutationMapper. MutationMapper will be installed to C:\Users[Your Username]\AppData\Local\MutationMapper\MutationMapper.exe.

UNINSTALL

Linux: Uninstall via your package manager (e.g. sudo apt-get remove MutationMapper).

Mac OS X: Drag the MutationMapperapplication from your Applications folder to the recycle bin.

Windows 7: MutationMapper should be installed to 'C:\Users[Your Username]\AppData\Local\MutationMapper\MutationMapper.exe'. To uninstall double-click the 'unins000.exe' file in this location. You can also access this location by right-clicking the MutationMapper application from the Start menu, selecting 'Properties' and clicking the 'Open File Location' button in the resulting window.

JAR FILE

To use the jar file download the MutationMapper_v2.1_jar.zip file and unzip. The jar can be run as normal (e.g. java -jar MutationMapper.jar) as long as it remains in the same folder as the enclosed 'lib' directory. Java version 1.8.0_45 or higher is required.

MutationMapper v2.0

This is the first release of MutationMapper since its rewrite as a multiplatform (Mac OS X, Linux and Windows) application.

All versions only work with 64-bit systems.

Using short sequences of wild type vs mutant DNA, MutationMapper will report the functional consequence of a given mutation, whether SNV:

...insertion:

...or deletion:

It can also be used for mapping sequences or CDS coordinates to genomic positions:

and to get mutation consequences from CDS nomenclature:

Results are reported in a detailed table, with annotations including the HGVS nomenclature, genomic position, overlap with any known variation in public databases and polyphen and SIFT predictions.

Results can be filtered to only show canonical, coding or RefSeq transcripts. The image below shows the results of four runs filtered to only show information from canonical transcripts:

For more information see the help documentation.

INSTALL

64 bit systems only

Linux: Download the MutationMapper-Linux64-2.0-1.x86_64.rpm (for RPM-based distros - e.g. CentOS), MutationMapper-Linux64-2.0.deb (for DEB based distros, e.g. Ubuntu) or MutationMapper-Linux64-2.0-1.pkg.tar.xz (Arch Linux) depending on your system and install via your package manager (e.g. sudo dpkg -i MutationMapper-Linux64-2.0.deb) or, if your distribution supports it, by double-clicking the downloaded package.

Mac OS X: Download the MutationMapper-MacOSX-2.0.dmg disk image. Double click to open the downloaded file and drag the MutationMapper application into your Applications folder where it can be opened by double clicking. On recent versions of Mac OS X you will need to access the 'Security & Privacy' settings in System Preferences to allow this app to be opened.

Windows: Download the MutationMapper-2.0-windows-installer.exe installer application. Double click the downloaded file and follow the instructions to install. This will also launch MutationMapper once installed. To launch in future it should be accessible from the Start menu->All Programs->MutationMapper. MutationMapper will be installed to C:\Users[Your Username]\AppData\Local\MutationMapper\MutationMapper.exe.

UNINSTALL

Linux: Uninstall via your package manager (e.g. sudo apt-get remove MutationMapper).

Mac OS X: Drag the MutationMapperapplication from your Applications folder to the recycle bin.

Windows 7: MutationMapper should be installed to 'C:\Users[Your Username]\AppData\Local\MutationMapper\MutationMapper.exe'. To uninstall double-click the 'unins000.exe' file in this location. You can also access this location by right-clicking the MutationMapper application from the Start menu, selecting 'Properties' and clicking the 'Open File Location' button in the resulting window.