Figure 3

PET extraction using the Extractor module. The process of PET extraction is initiated through the opening of 'Extractor' listed under the 'ToolSet'. Once a library is selected, library-specific parameters related to PET extraction will show up, such as spacer sequences and minimum/maximum PET length previously entered during library creation. Once the extraction parameters are confirmed or modified by the users, the DNA sequence file in FASTA format is browsed and uploaded. The 'sequencing center' accommodates different naming conventions for sequence IDs (used in input files) generated by different sequencing centers. The selection of a given naming convention method from the 'sequencing center' is needed for the system to properly parse individual sequences in groups of specific wells and plates for particular libraries. The user also needs to specify if the library is a GIS-PET or ChIP-PET library.