Keeping Pichia pastoris up to date

This book presents the Installation of GBrowse 2.39 and the re-implementation of the additional features implemented by Andreas Redl (Redl 2008) for GBrowse 1.69. The introduction presents an overview and a comparison of some of the free available genome browsers. The phylogeny of Pichia pastoris is outlined and reasons for choosing P. pastoris are presented and the additional features in the GBrowse ver-sion 1.69 are described. Further the changes in the GBrowse version 2.39, the installation of this version from scratch, starting with the OS, are described. The appendix contains the command list for the installation. The re-implementation of the additional features and the reasons for the selection of algorithms are presented, also the data preparation for the three strains DSMZ 70382, GS115 and CBS7435. The 'Discussion' section discusses the merits of manually curated GFF3 data files and the problems of automatically creates ones. Further some of the installation and data preparation problems are also presented. The 'Outlook' chapter suggests the implementation of some helper scripts and the exploit of the 'render farm' feature as expansion for the new GBrowse version 2.39.