\BOOKMARK [1][-]{section.1}{Introduction}{}% 1
\BOOKMARK [2][-]{subsection.1.1}{The parts of GenomeThreader}{section.1}% 2
\BOOKMARK [2][-]{subsection.1.2}{Structure of the Manual}{section.1}% 3
\BOOKMARK [1][-]{section.2}{Installation}{}% 4
\BOOKMARK [1][-]{section.3}{gth: Computing Gene Predictions}{}% 5
\BOOKMARK [2][-]{subsection.3.1}{Input Options}{section.3}% 6
\BOOKMARK [2][-]{subsection.3.2}{Parameter File Options}{section.3}% 7
\BOOKMARK [2][-]{subsection.3.3}{Strand Direction Options}{section.3}% 8
\BOOKMARK [2][-]{subsection.3.4}{Genomic Sequence Positions Options}{section.3}% 9
\BOOKMARK [2][-]{subsection.3.5}{Output Options}{section.3}% 10
\BOOKMARK [2][-]{subsection.3.6}{Data Preprocessing}{section.3}% 11
\BOOKMARK [2][-]{subsection.3.7}{Options of the Similarity Filter}{section.3}% 12
\BOOKMARK [2][-]{subsection.3.8}{Intron Cutout Technique Options}{section.3}% 13
\BOOKMARK [2][-]{subsection.3.9}{Advanced Options}{section.3}% 14
\BOOKMARK [3][-]{subsubsection.3.9.1}{Options for U12-type introns}{subsection.3.9}% 15
\BOOKMARK [3][-]{subsubsection.3.9.2}{Basic DP Algorithm Options}{subsection.3.9}% 16
\BOOKMARK [3][-]{subsubsection.3.9.3}{Short Exon/Intron Parameters}{subsection.3.9}% 17
\BOOKMARK [3][-]{subsubsection.3.9.4}{Special Parameters for the DP Algorithm}{subsection.3.9}% 18
\BOOKMARK [3][-]{subsubsection.3.9.5}{Options for Processing of ``raw'' Spliced Alignments}{subsection.3.9}% 19
\BOOKMARK [3][-]{subsubsection.3.9.6}{Spliced Alignment Filter}{subsection.3.9}% 20
\BOOKMARK [3][-]{subsubsection.3.9.7}{Advanced Similarity Filter Option}{subsection.3.9}% 21
\BOOKMARK [3][-]{subsubsection.3.9.8}{Interrupt Option}{subsection.3.9}% 22
\BOOKMARK [3][-]{subsubsection.3.9.9}{Options for Postprocessing of Predicted Gene Locations}{subsection.3.9}% 23
\BOOKMARK [3][-]{subsubsection.3.9.10}{Statistical Options}{subsection.3.9}% 24
\BOOKMARK [3][-]{subsubsection.3.9.11}{Miscellaneous Options}{subsection.3.9}% 25
\BOOKMARK [1][-]{section.4}{gthconsensus: Incremental Updates}{}% 26
\BOOKMARK [2][-]{subsection.4.1}{The Options of gthconsensus}{section.4}% 27
\BOOKMARK [1][-]{section.5}{gthsplit: Split Intermediate Files}{}% 28
\BOOKMARK [2][-]{subsection.5.1}{Applying gthsplit}{section.5}% 29
\BOOKMARK [2][-]{subsection.5.2}{The Script gthsplit2dim.sh}{section.5}% 30
\BOOKMARK [2][-]{subsection.5.3}{Applying gthsplit2dim.sh}{section.5}% 31
\BOOKMARK [1][-]{section.6}{gthgetseq: Get Fasta Sequences}{}% 32
\BOOKMARK [2][-]{subsection.6.1}{Applying gthgetseq}{section.6}% 33
\BOOKMARK [1][-]{section.7}{gthfilestat: Show Statistics}{}% 34
\BOOKMARK [2][-]{subsection.7.1}{Applying gthfilestat}{section.7}% 35
\BOOKMARK [1][-]{section.8}{gthbssmfileinfo: BSSM File Information}{}% 36
\BOOKMARK [1][-]{section.9}{gthbssmtrain: Train BSSMs}{}% 37
\BOOKMARK [2][-]{subsection.9.1}{Applying gthbssmtrain}{section.9}% 38
\BOOKMARK [1][-]{section.10}{gthbssmbuild: Build BSSM files}{}% 39
\BOOKMARK [2][-]{subsection.10.1}{The BSSM training data directory}{section.10}% 40
\BOOKMARK [1][-]{section.11}{gthclean.sh: Remove Indices}{}% 41
\BOOKMARK [1][-]{section.12}{Construction of the Indices}{}% 42
\BOOKMARK [1][-]{section.13}{Tutorial}{}% 43
\BOOKMARK [2][-]{subsection.13.1}{Mapping a Single EST on the A. thaliana Chromosome 1}{section.13}% 44
\BOOKMARK [2][-]{subsection.13.2}{Using the Intron Cutout Technique}{section.13}% 45
\BOOKMARK [2][-]{subsection.13.3}{Employing gthconsensus}{section.13}% 46
\BOOKMARK [1][-]{section.14}{Feedback}{}% 47
\BOOKMARK [1][-]{section.15}{Acknowledgements}{}% 48
\BOOKMARK [1][-]{section.16}{Recent Changes}{}% 49
\BOOKMARK [1][-]{section*.74}{References}{}% 50
\BOOKMARK [1][-]{section*.75}{Index}{}% 51
