Provided by: genometools_1.5.1-2ubuntu1_amd64
gt-eval - Compare annotation files and show accuracy measures (prediction vs. reference).
gt eval reference_file prediction_file
-nuc evaluate nucleotide level (memory consumption is proportional to the input file sizes) (default: yes) -ltr evaluate a LTR retrotransposon prediction instead of a gene prediction (all LTR_retrotransposon elements are considered to have an undetermined strand) (default: no) -ltrdelta set allowed delta for LTR borders to be considered equal (default: 20) -v be verbose (default: no) -o redirect output to specified file (default: undefined) -gzip write gzip compressed output file (default: no) -bzip2 write bzip2 compressed output file (default: no) -force force writing to output file (default: no) -help display help and exit -version display version information and exit
The program shows sensitivity and specificity values for certain feature types (e.g., gene, mRNA, and exon). For some feature types the number of missing and wrong features of that type is also shown. Thereby, “missing” means the numbe r of features of that type from the “reference” without overlap to a feature of that type from the “prediction”. Vice versa, “wrong” denotes the number of features of that type from the “prediction” without overlap to a feature of that type from the “reference”.
Report bugs to <firstname.lastname@example.org>. 10/07/2012 GT-EVAL(1)