=============================================== Program "gmhmmp_heuristic.pl" runs GeneMark.hmm with Heuristic models on single or multiple sequences in FASTA format. Version 1.1 Usage: gmhmmp_heuristic.pl [options] -s Optional parameters: -outfile output file name default: .lst -a write predicted protein sequence -n write nucleotide sequence of predicted genes -i initial probability of non-coding state -gcode genetic code default: 11; supported: 11, 4 and 1 -test installation test -verbose progress information on Output format: The output, protein coding region predictions for each sequence from the multiple FASTA sequences (the input) is provided in the following format: A. Header line marks the beginning of the prediction for a given single sequence It starts with "# " and continues with the FASTA definition line for that sequence For example: # >N_A0000001 B. List of predictions made by GeneMark.hmm with Heuristic models For example: GeneMark.hmm PROKARYOTIC (Version 2.6p) Sequence file name: seq, RBS: N Model file name: /home/alexl/b/heuristic_mod/heu_11_70.mod Model organism: Heuristic_model_for_genetic_code_11_and_GC_70 Thu Mar 6 15:49:38 2008 Predicted genes Gene Strand LeftEnd RightEnd Gene Class # Length 1 + 36 1040 1005 1 2 + 1037 2002 966 1 3 + 2070 3179 1110 1 4 + 3172 4287 1116 1 5 - 4342 4704 363 1 C. End of the prediction list is marked by string "#===" Error reporting: If sequence is too short (shorter than 40 nt) or unexpected sequence format is found, the error message will be printed in file in place of predicted genes. For example: # >test1 record ignored: short sequence #=== Note that the gene class column will not be informative for this application (it will always be Class 1). ===============================================