Readme for SpliceportScorer.jar and FeatureConverter.jar SpliceScorer: Scores possible donor and acceptor sites in a provided fasta file based on how likely they are to be true splicing donor or acceptor sites. Execution Command Sample: java -jar SpliceportScorer.jar -t 5 -f HPRT1.fasta -d donorFeatures.txt -a acceptorFeatures.txt -w 162 Options: -w: Window Size -t: Number of Threads(optimally number of processors avialable +1, default is 2)* -f: Input Fasta File -a: Acceptor Feature File (Spliceport 2.0 feature file type) -d: Donor Feature File (Spliceport 2.0 feature file type) -o: Output file *Optional Argument FeatureConverter: Converts Spliceport 1.0 feature files to Spliceport 2.0 feature files Execution Command Sample: java -jar FeatureConverter.jar -d donorFeatures.txt -a acceptorFeatures.txt -w 162 -od new_don.txt - oa new_acc.txt Options: -w: Window Size -a: Acceptor Feature File (Spliceport 1.0 feature file type) -d: Donor Feature File (Spliceport 1.0 feature file type) -oa: Output Acceptor File (Spliceport 2.0 feature file type) -od: Output Acceptor File (Spliceport 2.0 feature file type)