Table 4. Description of Java Objects used for bioinformatics analysis of transposon insertion sites.

Alignment	An object describing a BLAST alignment of a sequence read to the reference genome. Each line of tab-delimited BLAST output (i.e. set by BLAST option -outfmt 6) generates an Alignment object.
MuTag	An object that contains a list of the best scoring Alignment’s for a sequence query. I.e. each unique query (read) in the BLAST output generates a MuTag object. Only Alignment’s that have scores equal to top scoring Alignment for the query are retained.
Genome	A java Collections based database for Mu insertion data that contains a set of ordered lists of ChrLocus objects, one for each chromosome in the reference genome plus unplaced sequences, and a list of unique insertions (represented by Insertion objects) that have been mapped in the genome.
Insertion	A class describing the chromosome location(s) of a unique, mapped insertion site and the libraries and samples that contain reads from that insertion site. Its members include a unique identifier (e.g. muXXXXXX), a list of ChrLocus objects that describe possible locations of the insertion in the genome, and a list of Key objects that identify libraries and samples that contain reads from this insertion site. The ChrLocus list accommodates the fact that due to complexity of the genome (duplicated genes, etc) and limited read length some insertion sites map to multiple unresolved locations.
ChrLocus	An object describing a unique location in the reference genome. Member fields describe the chromosome and base pair position of a unique locus, a total count of the reads that have been mapped to that locus, and a count of reads that align in reverse orientation (allowing calculation of forward read count by subtraction). In addition, it contains a reference to the Insertion (unique insertion site) that is associated with this locus. A ChrLocus is uniquely assigned to one Insertion.
Key	An object that contains a count of reads assigned to each sample in a multiplex library. Member fields include the four-base barcode sequence, a unique library name, and a count of reads in the library that have that barcode.