Integrated proteogenomics database


We release the code to generate custom iPtgxDBs in the form of two java jar files and a public web server. Using a genome sequence file in FASTA format as input, the script iPtgxDB_insilico.jar can be executed to create a 6-frame translation (with additional options like alternative start codons). One or several existing reference genome annotations (blue containers) or results of ab initio gene prediction tools (green containers) can be processed with iPtgxDB_convert.jar to create several annotation.gff files (one per input file). All of these gff files are then combined on our public web server to create both the searchable iPtgxDB.fasta file and the iPtgxDB.gff file that contains all integrated annotations.

Software workflow illustration
Figure 5. Overview of the software modules to create iPtgxDBs.

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