Loading debian/man_src/align_dna.1.adoc 0 → 100644 +25 −0 Original line number Diff line number Diff line # align_dna(1) ## NAME align_dna - spliced align genomic sequence with cDNA ## SYNOPSIS *align_dna* [option ...] -datapath dir -bssmfile file ## OPTIONS *-genreverse*:: align reverse strand of genomic sequence default: no *-genrange*:: set aligned genomic range default: undefined *-help*:: display help and exit *-version*:: display version information and exit debian/man_src/gth.1.adoc +383 −89 Original line number Diff line number Diff line Loading @@ -2,7 +2,7 @@ ## NAME gth - calculate genome structures gth - predict genome structures ## SYNOPSIS Loading @@ -16,12 +16,17 @@ alignments to consensus spliced alignments. ## OPTIONS -genomic specify input files containing genomic sequences mandatory option -cdna specify input files containing cDNA/EST sequences -protein specify input files containing protein sequences -species specify species to select splice site model which is most appropriate; possible species: *-genomic* <file>:: specify input files containing genomic sequences (mandatory option) *-cdna* <file>:: specify input files containing cDNA/EST sequences *-protein* <file>:: specify input files containing protein sequences *-species* <species>:: specify species to select splice site model which is most appropriate; possible species: "human" "mouse" "rat" Loading @@ -35,87 +40,376 @@ alignments to consensus spliced alignments. "rice" "medicago" default: undefined -bssm read bssm parameter from file in the path given by the environment variable BSSMDIR default: undefined -scorematrix read amino acid substitution scoring matrix from file in the *-bssm*:: read bssm parameter from file in the path given by the environment variable BSSMDIR, default: undefined *-scorematrix*:: read amino acid substitution scoring matrix from file in the path given by the environment variable GTHDATADIR default: BLOSUM62 -translationtable set the codon translation table used for codon translation in *-translationtable*:: set the codon translation table used for codon translation in matching, DP, and output default: 1 -f analyze only forward strand of genomic sequences *-f*:: analyze only forward strand of genomic sequences default: no -r analyze only reverse strand of genomic sequences *-r*:: analyze only reverse strand of genomic sequences default: no -cdnaforward align only forward strand of cDNAs *-cdnaforward*:: align only forward strand of cDNAs default: no -frompos analyze genomic sequence from this position *-frompos*:: analyze genomic sequence from this position requires -topos or -width; counting from 1 on default: 0 -topos analyze genomic sequence to this position *-topos*:: analyze genomic sequence to this position requires -frompos; counting from 1 on default: 0 -width analyze only this width of genomic sequence *-width*:: analyze only this width of genomic sequence requires -frompos default: 0 -v be verbose *-v*:: be verbose default: no -xmlout show output in XML format *-xmlout*:: show output in XML format default: no -gff3out show output in GFF3 format *-gff3out*:: show output in GFF3 format default: no -md5ids show MD5 fingerprints as sequence IDs *-md5ids*:: show MD5 fingerprints as sequence IDs default: no -o redirect output to specified file *-o*:: redirect output to specified file default: undefined -gzip write gzip compressed output file *-gzip*:: write gzip compressed output file default: no *-bzip2*:: write bzip2 compressed output file default: no *-force*:: force writing to output file default: no -bzip2 write bzip2 compressed output file *-skipalignmentout*:: skip output of spliced alignments default: no -force force writing to output file *-mincutoffs*:: show full spliced alignments i.e., cutoffs mode for leading and terminal bases is MINIMAL default: no -gs2out output in old GeneSeqer2 format *-showintronmaxlen*:: set the maximum length of a fully shown intron If set to 0, all introns are shown completely default: 120 *-minorflen*:: set the minimum length of an ORF to be shown default: 64 *-startcodon*:: require than an ORF must begin with a start codon default: no -minmatchlen specify minimum match length (cDNA matching) *-finalstopcodon*:: require that the final ORF must end with a stop codon default: no *-showseqnums*:: show sequence numbers in output default: no *-pglgentemplate*:: show genomic template in PGL lines (switch off for backward compatibility) default: yes *-gs2out*:: output in old GeneSeqer2 format default: no *-maskpolyatails*:: mask poly(A) tails in cDNA/EST files default: no *-proteinsmap*:: specify smap file used for protein files default: protein *-noautoindex*:: do not create indices automatically except for the .dna.* files used for the DP. existence is not tested before an index is actually used! default: no *-createindicesonly*:: stop program flow after the indices have been created default: no *-skipindexcheck*:: skip index check (in preprocessing phase) default: no *-minmatchlen*:: specify minimum match length (cDNA matching) default: 20 -seedlength specify the seed length (cDNA matching) *-seedlength*:: specify the seed length (cDNA matching) default: 18 -exdrop specify the Xdrop value for edit distance extension (cDNA *-exdrop*:: specify the Xdrop value for edit distance extension (cDNA matching) default: 2 -prminmatchlen specify minimum match length (protein matches) *-prminmatchlen*:: specify minimum match length (protein matches) default: 24 -prseedlength specify seed length (protein matching) *-prseedlength*:: specify seed length (protein matching) default: 10 -prhdist specify Hamming distance (protein matching) *-prhdist*:: specify Hamming distance (protein matching) default: 4 -gcmaxgapwidth set the maximum gap width for global chains *-online*:: run the similarity filter online without using the complete index (increases runtime) default: no *-inverse*:: invert query and index in vmatch call default: no *-exact*:: use exact matches in the similarity filter default: no *-gcmaxgapwidth*:: set the maximum gap width for global chains defines approximately the maximum intron length set to 0 to allow for unlimited length in order to avoid false-positive exons (lonely exons) at the sequence ends, it is very important to set this parameter appropriately! default: 1000000 -gcmincoverage set the minimum coverage of global chains regarding to the *-gcmincoverage*:: set the minimum coverage of global chains regarding to the reference sequence default: 50 -paralogs compute paralogous genes (different chaining procedure) *-paralogs*:: compute paralogous genes (different chaining procedure) default: no *-enrichchains*:: enrich genomic sequence part of global chains with additional matches default: no -introncutout enable the intron cutout technique *-introncutout*:: enable the intron cutout technique default: no -fastdp use jump table to increase speed of DP calculation *-fastdp*:: use jump table to increase speed of DP calculation default: no -autointroncutout set the automatic intron cutout matrix size in megabytes and *-autointroncutout*:: set the automatic intron cutout matrix size in megabytes and enable the automatic intron cutout technique default: 0 -intermediate stop after calculation of spliced alignments and output *-icinitialdelta*:: set the initial delta used for intron cutouts default: 50 *-iciterations*:: set the number of intron cutout iterations default: 2 *-icdeltaincrease*:: set the delta increase during every iteration default: 50 *-icminremintronlen*:: set the minimum remaining intron length for an intron to be cut out default: 10 *-nou12intronmodel*:: disable the U12-type intron model default: no *-u12donorprob*:: set the probability for perfect U12-type donor sites default: 0.99 *-u12donorprob1mism*:: set the prob. for U12-type donor w. 1 mismatch default: 0.90 *-probies*:: set the initial exon state probability default: 0.50 *-probdelgen*:: set the genomic sequence deletion probability default: 0.03 *-identityweight*:: set the pairs of identical characters weight default: 2.00 *-mismatchweight*:: set the weight for mismatching characters default: -2.00 *-undetcharweight*:: set the weight for undetermined characters default: 0.00 *-deletionweight*:: set the weight for deletions default: -5.00 *-dpminexonlen*:: set the minimum exon length for the DP default: 5 *-dpminintronlen*:: set the minimum intron length for the DP default: 50 *-shortexonpenal*:: set the short exon penalty default: 100.00 *-shortintronpenal*:: set the short intron penalty default: 100.00 *-wzerotransition*:: set the zero transition weights window size default: 80 *-wdecreasedoutput*:: set the decreased output weights window size default: 80 *-leadcutoffsmode*:: set the cutoffs mode for leading bases can be either RELAXED, STRICT, or MINIMAL default: RELAXED *-termcutoffsmode*:: set the cutoffs mode for terminal bases can be either RELAXED, STRICT, or MINIMAL default: STRICT *-cutoffsminexonlen*:: set the cutoffs minimum exon length default: 5 *-scoreminexonlen*:: set the score minimum exon length default: 50 *-minaveragessp*:: set the minimum average splice site prob. default: 0.50 *-duplicatecheck*:: criterion used to check for spliced alignment duplicates, choose from none|id|desc|seq|both default: both *-minalignmentscore*:: set the minimum alignment score for spliced alignments to be included into the set of spliced alignments default: 0.00 *-maxalignmentscore*:: set the maximum alignment score for spliced alignments to be included into the set of spliced alignments default: 1.00 *-mincoverage*:: set the minimum coverage for spliced alignments to be included into the set of spliced alignments default: 0.00 *-maxcoverage*:: set the maximum coverage for spliced alignments to be included into the set of spliced alignments default: 9999.99 *-intermediate*:: stop after calculation of spliced alignments and output results in reusable XML format. Do not process this output yourself, use the ``normal'' XML output instead! default: no -first set the maximum number of spliced alignments per genomic DNA *-sortags*:: sort alternative gene structures according to the weighted mean of the average exon score and the average splice site probability default: no *-sortagswf*:: set the weight factor for the sorting of AGSs default: 1.00 *-exondistri*:: show the exon length distribution default: no *-introndistri*:: show the intron length distribution default: no *-refseqcovdistri*:: show the reference sequence coverage distribution default: no *-first*:: set the maximum number of spliced alignments per genomic DNA input. Set to 0 for unlimited number. default: 0 -help display help for basic options and exit -help+ display help for all options and exit -version display version information and exit *-help*:: display help for basic options and exit *-help+*:: display help for all options and exit *-version*:: display version information and exit debian/man_src/gthbssmbuild.1.adoc 0 → 100644 +46 −0 Original line number Diff line number Diff line # gthbssmbuild(1) ## NAME gthbssmbuild - build splice site model ## SYNOPSIS *gthbssmbuild* [option ...] genomic_file cDNA_file ## DESCRIPTION Build a BSSM file from a directory tree containing the training data. ## OPTIONS *-bssmfile*:: specify name of BSSM file to store parameters in default: undefined *-datapath*:: specify root of species-specific training data directory tree default: undefined *-gtdonor*:: train GT donor model default: no *-gcdonor*:: train GC donor model default: no *-agacceptor*:: train AG acceptor model default: no *-gzip*:: use gzip'ed input files default: no *-help*:: display help and exit *-version*:: display version information and exit Loading
debian/man_src/align_dna.1.adoc 0 → 100644 +25 −0 Original line number Diff line number Diff line # align_dna(1) ## NAME align_dna - spliced align genomic sequence with cDNA ## SYNOPSIS *align_dna* [option ...] -datapath dir -bssmfile file ## OPTIONS *-genreverse*:: align reverse strand of genomic sequence default: no *-genrange*:: set aligned genomic range default: undefined *-help*:: display help and exit *-version*:: display version information and exit
debian/man_src/gth.1.adoc +383 −89 Original line number Diff line number Diff line Loading @@ -2,7 +2,7 @@ ## NAME gth - calculate genome structures gth - predict genome structures ## SYNOPSIS Loading @@ -16,12 +16,17 @@ alignments to consensus spliced alignments. ## OPTIONS -genomic specify input files containing genomic sequences mandatory option -cdna specify input files containing cDNA/EST sequences -protein specify input files containing protein sequences -species specify species to select splice site model which is most appropriate; possible species: *-genomic* <file>:: specify input files containing genomic sequences (mandatory option) *-cdna* <file>:: specify input files containing cDNA/EST sequences *-protein* <file>:: specify input files containing protein sequences *-species* <species>:: specify species to select splice site model which is most appropriate; possible species: "human" "mouse" "rat" Loading @@ -35,87 +40,376 @@ alignments to consensus spliced alignments. "rice" "medicago" default: undefined -bssm read bssm parameter from file in the path given by the environment variable BSSMDIR default: undefined -scorematrix read amino acid substitution scoring matrix from file in the *-bssm*:: read bssm parameter from file in the path given by the environment variable BSSMDIR, default: undefined *-scorematrix*:: read amino acid substitution scoring matrix from file in the path given by the environment variable GTHDATADIR default: BLOSUM62 -translationtable set the codon translation table used for codon translation in *-translationtable*:: set the codon translation table used for codon translation in matching, DP, and output default: 1 -f analyze only forward strand of genomic sequences *-f*:: analyze only forward strand of genomic sequences default: no -r analyze only reverse strand of genomic sequences *-r*:: analyze only reverse strand of genomic sequences default: no -cdnaforward align only forward strand of cDNAs *-cdnaforward*:: align only forward strand of cDNAs default: no -frompos analyze genomic sequence from this position *-frompos*:: analyze genomic sequence from this position requires -topos or -width; counting from 1 on default: 0 -topos analyze genomic sequence to this position *-topos*:: analyze genomic sequence to this position requires -frompos; counting from 1 on default: 0 -width analyze only this width of genomic sequence *-width*:: analyze only this width of genomic sequence requires -frompos default: 0 -v be verbose *-v*:: be verbose default: no -xmlout show output in XML format *-xmlout*:: show output in XML format default: no -gff3out show output in GFF3 format *-gff3out*:: show output in GFF3 format default: no -md5ids show MD5 fingerprints as sequence IDs *-md5ids*:: show MD5 fingerprints as sequence IDs default: no -o redirect output to specified file *-o*:: redirect output to specified file default: undefined -gzip write gzip compressed output file *-gzip*:: write gzip compressed output file default: no *-bzip2*:: write bzip2 compressed output file default: no *-force*:: force writing to output file default: no -bzip2 write bzip2 compressed output file *-skipalignmentout*:: skip output of spliced alignments default: no -force force writing to output file *-mincutoffs*:: show full spliced alignments i.e., cutoffs mode for leading and terminal bases is MINIMAL default: no -gs2out output in old GeneSeqer2 format *-showintronmaxlen*:: set the maximum length of a fully shown intron If set to 0, all introns are shown completely default: 120 *-minorflen*:: set the minimum length of an ORF to be shown default: 64 *-startcodon*:: require than an ORF must begin with a start codon default: no -minmatchlen specify minimum match length (cDNA matching) *-finalstopcodon*:: require that the final ORF must end with a stop codon default: no *-showseqnums*:: show sequence numbers in output default: no *-pglgentemplate*:: show genomic template in PGL lines (switch off for backward compatibility) default: yes *-gs2out*:: output in old GeneSeqer2 format default: no *-maskpolyatails*:: mask poly(A) tails in cDNA/EST files default: no *-proteinsmap*:: specify smap file used for protein files default: protein *-noautoindex*:: do not create indices automatically except for the .dna.* files used for the DP. existence is not tested before an index is actually used! default: no *-createindicesonly*:: stop program flow after the indices have been created default: no *-skipindexcheck*:: skip index check (in preprocessing phase) default: no *-minmatchlen*:: specify minimum match length (cDNA matching) default: 20 -seedlength specify the seed length (cDNA matching) *-seedlength*:: specify the seed length (cDNA matching) default: 18 -exdrop specify the Xdrop value for edit distance extension (cDNA *-exdrop*:: specify the Xdrop value for edit distance extension (cDNA matching) default: 2 -prminmatchlen specify minimum match length (protein matches) *-prminmatchlen*:: specify minimum match length (protein matches) default: 24 -prseedlength specify seed length (protein matching) *-prseedlength*:: specify seed length (protein matching) default: 10 -prhdist specify Hamming distance (protein matching) *-prhdist*:: specify Hamming distance (protein matching) default: 4 -gcmaxgapwidth set the maximum gap width for global chains *-online*:: run the similarity filter online without using the complete index (increases runtime) default: no *-inverse*:: invert query and index in vmatch call default: no *-exact*:: use exact matches in the similarity filter default: no *-gcmaxgapwidth*:: set the maximum gap width for global chains defines approximately the maximum intron length set to 0 to allow for unlimited length in order to avoid false-positive exons (lonely exons) at the sequence ends, it is very important to set this parameter appropriately! default: 1000000 -gcmincoverage set the minimum coverage of global chains regarding to the *-gcmincoverage*:: set the minimum coverage of global chains regarding to the reference sequence default: 50 -paralogs compute paralogous genes (different chaining procedure) *-paralogs*:: compute paralogous genes (different chaining procedure) default: no *-enrichchains*:: enrich genomic sequence part of global chains with additional matches default: no -introncutout enable the intron cutout technique *-introncutout*:: enable the intron cutout technique default: no -fastdp use jump table to increase speed of DP calculation *-fastdp*:: use jump table to increase speed of DP calculation default: no -autointroncutout set the automatic intron cutout matrix size in megabytes and *-autointroncutout*:: set the automatic intron cutout matrix size in megabytes and enable the automatic intron cutout technique default: 0 -intermediate stop after calculation of spliced alignments and output *-icinitialdelta*:: set the initial delta used for intron cutouts default: 50 *-iciterations*:: set the number of intron cutout iterations default: 2 *-icdeltaincrease*:: set the delta increase during every iteration default: 50 *-icminremintronlen*:: set the minimum remaining intron length for an intron to be cut out default: 10 *-nou12intronmodel*:: disable the U12-type intron model default: no *-u12donorprob*:: set the probability for perfect U12-type donor sites default: 0.99 *-u12donorprob1mism*:: set the prob. for U12-type donor w. 1 mismatch default: 0.90 *-probies*:: set the initial exon state probability default: 0.50 *-probdelgen*:: set the genomic sequence deletion probability default: 0.03 *-identityweight*:: set the pairs of identical characters weight default: 2.00 *-mismatchweight*:: set the weight for mismatching characters default: -2.00 *-undetcharweight*:: set the weight for undetermined characters default: 0.00 *-deletionweight*:: set the weight for deletions default: -5.00 *-dpminexonlen*:: set the minimum exon length for the DP default: 5 *-dpminintronlen*:: set the minimum intron length for the DP default: 50 *-shortexonpenal*:: set the short exon penalty default: 100.00 *-shortintronpenal*:: set the short intron penalty default: 100.00 *-wzerotransition*:: set the zero transition weights window size default: 80 *-wdecreasedoutput*:: set the decreased output weights window size default: 80 *-leadcutoffsmode*:: set the cutoffs mode for leading bases can be either RELAXED, STRICT, or MINIMAL default: RELAXED *-termcutoffsmode*:: set the cutoffs mode for terminal bases can be either RELAXED, STRICT, or MINIMAL default: STRICT *-cutoffsminexonlen*:: set the cutoffs minimum exon length default: 5 *-scoreminexonlen*:: set the score minimum exon length default: 50 *-minaveragessp*:: set the minimum average splice site prob. default: 0.50 *-duplicatecheck*:: criterion used to check for spliced alignment duplicates, choose from none|id|desc|seq|both default: both *-minalignmentscore*:: set the minimum alignment score for spliced alignments to be included into the set of spliced alignments default: 0.00 *-maxalignmentscore*:: set the maximum alignment score for spliced alignments to be included into the set of spliced alignments default: 1.00 *-mincoverage*:: set the minimum coverage for spliced alignments to be included into the set of spliced alignments default: 0.00 *-maxcoverage*:: set the maximum coverage for spliced alignments to be included into the set of spliced alignments default: 9999.99 *-intermediate*:: stop after calculation of spliced alignments and output results in reusable XML format. Do not process this output yourself, use the ``normal'' XML output instead! default: no -first set the maximum number of spliced alignments per genomic DNA *-sortags*:: sort alternative gene structures according to the weighted mean of the average exon score and the average splice site probability default: no *-sortagswf*:: set the weight factor for the sorting of AGSs default: 1.00 *-exondistri*:: show the exon length distribution default: no *-introndistri*:: show the intron length distribution default: no *-refseqcovdistri*:: show the reference sequence coverage distribution default: no *-first*:: set the maximum number of spliced alignments per genomic DNA input. Set to 0 for unlimited number. default: 0 -help display help for basic options and exit -help+ display help for all options and exit -version display version information and exit *-help*:: display help for basic options and exit *-help+*:: display help for all options and exit *-version*:: display version information and exit
debian/man_src/gthbssmbuild.1.adoc 0 → 100644 +46 −0 Original line number Diff line number Diff line # gthbssmbuild(1) ## NAME gthbssmbuild - build splice site model ## SYNOPSIS *gthbssmbuild* [option ...] genomic_file cDNA_file ## DESCRIPTION Build a BSSM file from a directory tree containing the training data. ## OPTIONS *-bssmfile*:: specify name of BSSM file to store parameters in default: undefined *-datapath*:: specify root of species-specific training data directory tree default: undefined *-gtdonor*:: train GT donor model default: no *-gcdonor*:: train GC donor model default: no *-agacceptor*:: train AG acceptor model default: no *-gzip*:: use gzip'ed input files default: no *-help*:: display help and exit *-version*:: display version information and exit
