New Features in Alamut version 1.5 (May 2009)
- Easier installation: settings from a previous installed version of Alamut can now be retrieved automatically.
- New gene query functionality: users can now type in common gene names (not only official symbols) or any gene-related words to query the database.
- New mutation import functionality: lists of variant annotations prepared in tabulated files can now be imported, displayed and further edited inside Alamut.
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Enhanced splicing module:
- NNSPLICE from fruitfly.org can now be interrogated transparently from Alamut and its results displayed seamlessly in the graphical interface.
- The sequence range analyzed by the splicing module can now be set interactively.
- Sequence coordinates are now displayed.
- Splicing method scores can now be displayed individually.
- Tabular splicing reports can now be generated.
- Preferred transcripts: when a gene has multiple transcripts, one of them can now be set as the "preferred transcript" and selected by default.
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Usability enhancements:
- New click-and-drag behavior in the main window and in the splicing window: just click and move the cursor to smoothly scroll the view.
- New 'Go to exon...' quick navigation button.
- Variant colors in the graphical display are now based on their annotated pathogenicity
- Variants can now be classified using the 4-classes scheme suggested by the CMGS/VKGL Practice guidelines for the interpretation of UVs.
- Two variant annotation fields have been added: results of RNA analysis and X-inactivation profile.
- New variants created in the software are no longer saved systematically.
- Mutation reports can now be saved.
- SNPs can now be exported to tabular files.
- Orthologue multiple alignments can now be exported to FASTA files.
Version 1.51 (Nov. 2009)
- Fixed bug: clicking on a nsSNP sometimes displayed wrong AA.
- Changed the id/password protection scheme to an id/license key scheme.
Version 1.52 (Dec. 2009)
- Gene flanking regions can now be extended on demand.
Version 1.53 (Dec. 2009)
- Fixed problems with genes having only one coding exon.
Version 1.54 (June 2010)
- Fixed bug where GeneSplicer predictions where shifted left if
analyzed segment started
at the 5' locus boundary. - Extra-genic nucleotides now numbered according to HGVS recommandations.
See the Alamut 1.5 documentation