Author: sascha-guest Date: 2013-02-23 09:50:39 +0000 (Sat, 23 Feb 2013) New Revision: 13066
Modified: trunk/packages/aragorn/trunk/debian/changelog trunk/packages/aragorn/trunk/debian/man/aragorn.1 trunk/packages/aragorn/trunk/debian/manpage.1.src trunk/packages/aragorn/trunk/debian/patches/series trunk/packages/aragorn/trunk/debian/watch Log: adjust for 1.2.36, waiting for upstream to publish source Modified: trunk/packages/aragorn/trunk/debian/changelog =================================================================== --- trunk/packages/aragorn/trunk/debian/changelog 2013-02-23 09:50:24 UTC (rev 13065) +++ trunk/packages/aragorn/trunk/debian/changelog 2013-02-23 09:50:39 UTC (rev 13066) @@ -1,5 +1,5 @@ -aragorn (1.2.34-1) unstable; urgency=low +aragorn (1.2.36-1) unstable; urgency=low * Initial release (Closes: #nnnn) - -- Sascha Steinbiss <steinb...@zbh.uni-hamburg.de> Wed, 06 Feb 2013 10:02:30 +0100 + -- Sascha Steinbiss <steinb...@zbh.uni-hamburg.de> Wed, 16 Feb 2013 10:02:30 +0100 Modified: trunk/packages/aragorn/trunk/debian/man/aragorn.1 =================================================================== --- trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-02-23 09:50:24 UTC (rev 13065) +++ trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-02-23 09:50:39 UTC (rev 13066) @@ -2,12 +2,12 @@ .\" Title: aragorn .\" Author: [see the "AUTHORS" section] .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/> -.\" Date: 02/09/2013 +.\" Date: 02/23/2013 .\" Manual: \ \& .\" Source: \ \& .\" Language: English .\" -.TH "ARAGORN" "1" "02/09/2013" "\ \&" "\ \&" +.TH "ARAGORN" "1" "02/23/2013" "\ \&" "\ \&" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- @@ -117,7 +117,10 @@ strand of each sequence\&. \-ps Lower scoring thresholds to 95% of default levels\&. \-ps<num> Change scoring thresholds to <num> percent of default levels\&. -\-rp Report possible pseudogenes (normalised score < 100)\&. +\-rp Flag possible pseudogenes (score < 100 or tRNA anticodon + loop <> 7 bases long)\&. Note that genes with score < 100 + will not be detected or flagged if scoring thresholds are not + also changed to below 100% (see \-ps switch)\&. \-seq Print out primary sequence\&. \-br Show secondary structure of tRNA gene primary sequence using round brackets\&. @@ -161,9 +164,9 @@ <filename> is assumed to contain one or more sequences in FASTA format\&. Results of the search are printed to STDOUT\&. All switches are optional and case\-insensitive\&. Unless \-i is specified, tRNA genes containing introns are not detected\&. .SH "AUTHORS" .sp -Bjorn Canback <bcanback@acgt\&.se>, Dean Laslett <gaiaquark@gmail\&.com > +Bjorn Canback <bcanback@acgt\&.se>, Dean Laslett <gaiaquark@gmail\&.com> .SH "REFERENCES" .sp Laslett, D\&. and Canback, B\&. (2004) ARAGORN, a program for the detection of transfer RNA and transfer\-messenger RNA genes in nucleotide sequences Nucleic Acids Research, 32;11\-16 .sp -Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&. +Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&. Modified: trunk/packages/aragorn/trunk/debian/manpage.1.src =================================================================== --- trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-02-23 09:50:24 UTC (rev 13065) +++ trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-02-23 09:50:39 UTC (rev 13066) @@ -1,166 +1,169 @@ -ARAGORN(1) -========== - -NAME ----- - -aragorn - detect tRNA genes in nucleotide sequences - - -SYNOPSIS --------- - -*aragorn* -v -s -d -c -l -j -a -q -rn -w -ifro<min>,<max> -t -m -mt - -gc -tv -seq -br -fasta -fo -o <outfile> <filename> - - -OPTIONS -------- - - -m Search for tmRNA genes. - -t Search for tRNA genes. - By default, all are detected. If one of - -m or -t is specified, then the other - is not detected unless specified as well. - -mt Search for Metazoan mitochondrial tRNA genes. - tRNA genes with introns not detected. -i,-sr switchs - ignored. Composite Metazoan mitochondrial - genetic code used. - -mtmam Search for Mammalian mitochondrial tRNA - genes. -i,-sr switchs ignored. -tv switch set. - Mammalian mitochondrial genetic code used. - -mtx Same as -mt but low scoring tRNA genes are - not reported. - -mtd Overlapping metazoan mitochondrial tRNA genes - on opposite strands are reported. - -gc<num> Use the GenBank transl_table = <num> genetic code. - -gcstd Use standard genetic code. - -gcmet Use composite Metazoan mitochondrial genetic code. - -gcvert Use Vertebrate mitochondrial genetic code. - -gcinvert Use Invertebrate mitochondrial genetic code. - -gcyeast Use Yeast mitochondrial genetic code. - -gcprot Use Mold/Protozoan/Coelenterate mitochondrial genetic code. - -gcciliate Use Ciliate genetic code. - -gcflatworm Use Echinoderm/Flatworm mitochondrial genetic code - -gceuplot Use Euplotid genetic code. - -gcbact Use Bacterial/Plant Chloroplast genetic code. - -gcaltyeast Use alternative Yeast genetic code. - -gcascid Use Ascidian Mitochondrial genetic code. - -gcaltflat Use alternative Flatworm Mitochondrial genetic code. - -gcblep Use Blepharisma genetic code. - -gcchloroph Use Chlorophycean Mitochondrial genetic code. - -gctrem Use Trematode Mitochondrial genetic code. - -gcscen Use Scenedesmus obliquus Mitochondrial genetic code. - -gcthraust Use Thraustochytrium Mitochondrial genetic code. - Individual modifications can be appended using - ,BBB=<aa> B = A,C,G, or T. <aa> is the three letter - code for an amino-acid. More than one modification - can be specified. eg -gcvert,aga=Trp,agg=Trp uses - the Vertebrate Mitochondrial code and the codons - AGA and AGG changed to Tryptophan. - -tv Do not search for mitochondrial TV replacement - loop tRNA genes. Only relevant if -mt used. - -c7 Search for tRNA genes with 7 base C-loops only. - -i Search for tRNA genes with introns in - anticodon loop with maximum length 3000 - bases. Minimum intron length is 0 bases. - Ignored if -m is specified. - -i<max> Search for tRNA genes with introns in - anticodon loop with maximum length <max> - bases. Minimum intron length is 0 bases. - Ignored if -m is specified. - -i<min>,<max> Search for tRNA genes with introns in - anticodon loop with maximum length <max> - bases, and minimum length <min> bases. - Ignored if -m is specified. - -io Same as -i, but allow tRNA genes with long - introns to overlap shorter tRNA genes. - -if Same as -i, but fix intron between positions - 37 and 38 on C-loop (one base after anticodon). - -ifo Same as -if and -io combined. - -ir Same as -i, but report tRNA genes with minimum - length <min> bases rather than search for - tRNA genes with minimum length <min> bases. - With this switch, <min> acts as an output filter, - minimum intron length for searching is still 0 bases. - -c Assume that each sequence has a circular - topology. Search wraps around each end. - Default setting. - -l Assume that each sequence has a linear - topology. Search does not wrap. - -d Double. Search both strands of each - sequence. Default setting. - -s or -s+ Single. Do not search the complementary - (antisense) strand of each sequence. - -sc or -s- Single complementary. Do not search the sense - strand of each sequence. - -ps Lower scoring thresholds to 95% of default levels. - -ps<num> Change scoring thresholds to <num> percent of default levels. - -rp Report possible pseudogenes (normalised score < 100). - -seq Print out primary sequence. - -br Show secondary structure of tRNA gene primary sequence - using round brackets. - -fasta Print out primary sequence in fasta format. - -fo Print out primary sequence in fasta format only - (no secondary structure). - -fon Same as -fo, with sequence and gene numbering in header. - -fos Same as -fo, with no spaces in header. - -fons Same as -fo, with sequence and gene numbering, but no spaces. - -w Print out in Batch mode. - -ss Use the stricter canonical 1-2 bp spacer1 and - 1 bp spacer2. Ignored if -mt set. Default is to - allow 3 bp spacer1 and 0-2 bp spacer2, which may - degrade selectivity.\n"); - -v Verbose. Prints out information during - search to STDERR. - -a Print out tRNA domain for tmRNA genes. - -a7 Restrict tRNA astem length to a maximum of 7 bases - -aa Display message if predicted iso-acceptor species - does not match species in sequence name (if present). - -j Display 4-base sequence on 3' end of astem - regardless of predicted amino-acyl acceptor length. - -jr Allow some divergence of 3' amino-acyl acceptor - sequence from NCCA. - -jr4 Allow some divergence of 3' amino-acyl acceptor - sequence from NCCA, and display 4 bases. - -q Dont print configuration line (which switchs - and files were used). - -rn Repeat sequence name before summary information. - -O <outfile> Print output to <outfile>. If <outfile> - already exists, it is overwritten. By default - all output goes to stdout. - -DESCRIPTION ------------ - -aragorn detects tRNA, mtRNA, and tmRNA genes. -A minimum requirement is at least a 32 bit compiler architecture -(variable types int and unsigned int are at least 4 bytes long). - -<filename> is assumed to contain one or more sequences -in FASTA format. Results of the search are printed to -STDOUT. All switches are optional and case-insensitive. -Unless -i is specified, tRNA genes containing introns -are not detected. - - -AUTHORS ------- - -Bjorn Canback <bcanb...@acgt.se>, Dean Laslett <gaiaqu...@gmail.com > - - -REFERENCES ----------- - -Laslett, D. and Canback, B. (2004) ARAGORN, a -program for the detection of transfer RNA and transfer-messenger -RNA genes in nucleotide sequences -Nucleic Acids Research, 32;11-16 - -Laslett, D. and Canback, B. (2008) ARWEN: a -program to in metazoan mitochondrial -nucleotide sequences -Bioinformatics, 24(2); 172-175. - - +ARAGORN(1) +========== + +NAME +---- + +aragorn - detect tRNA genes in nucleotide sequences + + +SYNOPSIS +-------- + +*aragorn* -v -s -d -c -l -j -a -q -rn -w -ifro<min>,<max> -t -m -mt + -gc -tv -seq -br -fasta -fo -o <outfile> <filename> + + +OPTIONS +------- + + -m Search for tmRNA genes. + -t Search for tRNA genes. + By default, all are detected. If one of + -m or -t is specified, then the other + is not detected unless specified as well. + -mt Search for Metazoan mitochondrial tRNA genes. + tRNA genes with introns not detected. -i,-sr switchs + ignored. Composite Metazoan mitochondrial + genetic code used. + -mtmam Search for Mammalian mitochondrial tRNA + genes. -i,-sr switchs ignored. -tv switch set. + Mammalian mitochondrial genetic code used. + -mtx Same as -mt but low scoring tRNA genes are + not reported. + -mtd Overlapping metazoan mitochondrial tRNA genes + on opposite strands are reported. + -gc<num> Use the GenBank transl_table = <num> genetic code. + -gcstd Use standard genetic code. + -gcmet Use composite Metazoan mitochondrial genetic code. + -gcvert Use Vertebrate mitochondrial genetic code. + -gcinvert Use Invertebrate mitochondrial genetic code. + -gcyeast Use Yeast mitochondrial genetic code. + -gcprot Use Mold/Protozoan/Coelenterate mitochondrial genetic code. + -gcciliate Use Ciliate genetic code. + -gcflatworm Use Echinoderm/Flatworm mitochondrial genetic code + -gceuplot Use Euplotid genetic code. + -gcbact Use Bacterial/Plant Chloroplast genetic code. + -gcaltyeast Use alternative Yeast genetic code. + -gcascid Use Ascidian Mitochondrial genetic code. + -gcaltflat Use alternative Flatworm Mitochondrial genetic code. + -gcblep Use Blepharisma genetic code. + -gcchloroph Use Chlorophycean Mitochondrial genetic code. + -gctrem Use Trematode Mitochondrial genetic code. + -gcscen Use Scenedesmus obliquus Mitochondrial genetic code. + -gcthraust Use Thraustochytrium Mitochondrial genetic code. + Individual modifications can be appended using + ,BBB=<aa> B = A,C,G, or T. <aa> is the three letter + code for an amino-acid. More than one modification + can be specified. eg -gcvert,aga=Trp,agg=Trp uses + the Vertebrate Mitochondrial code and the codons + AGA and AGG changed to Tryptophan. + -tv Do not search for mitochondrial TV replacement + loop tRNA genes. Only relevant if -mt used. + -c7 Search for tRNA genes with 7 base C-loops only. + -i Search for tRNA genes with introns in + anticodon loop with maximum length 3000 + bases. Minimum intron length is 0 bases. + Ignored if -m is specified. + -i<max> Search for tRNA genes with introns in + anticodon loop with maximum length <max> + bases. Minimum intron length is 0 bases. + Ignored if -m is specified. + -i<min>,<max> Search for tRNA genes with introns in + anticodon loop with maximum length <max> + bases, and minimum length <min> bases. + Ignored if -m is specified. + -io Same as -i, but allow tRNA genes with long + introns to overlap shorter tRNA genes. + -if Same as -i, but fix intron between positions + 37 and 38 on C-loop (one base after anticodon). + -ifo Same as -if and -io combined. + -ir Same as -i, but report tRNA genes with minimum + length <min> bases rather than search for + tRNA genes with minimum length <min> bases. + With this switch, <min> acts as an output filter, + minimum intron length for searching is still 0 bases. + -c Assume that each sequence has a circular + topology. Search wraps around each end. + Default setting. + -l Assume that each sequence has a linear + topology. Search does not wrap. + -d Double. Search both strands of each + sequence. Default setting. + -s or -s+ Single. Do not search the complementary + (antisense) strand of each sequence. + -sc or -s- Single complementary. Do not search the sense + strand of each sequence. + -ps Lower scoring thresholds to 95% of default levels. + -ps<num> Change scoring thresholds to <num> percent of default levels. + -rp Flag possible pseudogenes (score < 100 or tRNA anticodon + loop <> 7 bases long). Note that genes with score < 100 + will not be detected or flagged if scoring thresholds are not + also changed to below 100% (see -ps switch). + -seq Print out primary sequence. + -br Show secondary structure of tRNA gene primary sequence + using round brackets. + -fasta Print out primary sequence in fasta format. + -fo Print out primary sequence in fasta format only + (no secondary structure). + -fon Same as -fo, with sequence and gene numbering in header. + -fos Same as -fo, with no spaces in header. + -fons Same as -fo, with sequence and gene numbering, but no spaces. + -w Print out in Batch mode. + -ss Use the stricter canonical 1-2 bp spacer1 and + 1 bp spacer2. Ignored if -mt set. Default is to + allow 3 bp spacer1 and 0-2 bp spacer2, which may + degrade selectivity.\n"); + -v Verbose. Prints out information during + search to STDERR. + -a Print out tRNA domain for tmRNA genes. + -a7 Restrict tRNA astem length to a maximum of 7 bases + -aa Display message if predicted iso-acceptor species + does not match species in sequence name (if present). + -j Display 4-base sequence on 3' end of astem + regardless of predicted amino-acyl acceptor length. + -jr Allow some divergence of 3' amino-acyl acceptor + sequence from NCCA. + -jr4 Allow some divergence of 3' amino-acyl acceptor + sequence from NCCA, and display 4 bases. + -q Dont print configuration line (which switchs + and files were used). + -rn Repeat sequence name before summary information. + -O <outfile> Print output to <outfile>. If <outfile> + already exists, it is overwritten. By default + all output goes to stdout. + +DESCRIPTION +----------- + +aragorn detects tRNA, mtRNA, and tmRNA genes. +A minimum requirement is at least a 32 bit compiler architecture +(variable types int and unsigned int are at least 4 bytes long). + +<filename> is assumed to contain one or more sequences +in FASTA format. Results of the search are printed to +STDOUT. All switches are optional and case-insensitive. +Unless -i is specified, tRNA genes containing introns +are not detected. + + +AUTHORS +------ + +Bjorn Canback <bcanb...@acgt.se>, Dean Laslett <gaiaqu...@gmail.com> + + +REFERENCES +---------- + +Laslett, D. and Canback, B. (2004) ARAGORN, a +program for the detection of transfer RNA and transfer-messenger +RNA genes in nucleotide sequences +Nucleic Acids Research, 32;11-16 + +Laslett, D. and Canback, B. (2008) ARWEN: a +program to detect tRNA genes in metazoan mitochondrial +nucleotide sequences +Bioinformatics, 24(2); 172-175. + + Modified: trunk/packages/aragorn/trunk/debian/patches/series =================================================================== --- trunk/packages/aragorn/trunk/debian/patches/series 2013-02-23 09:50:24 UTC (rev 13065) +++ trunk/packages/aragorn/trunk/debian/patches/series 2013-02-23 09:50:39 UTC (rev 13066) @@ -1,2 +0,0 @@ -formatstrings -hardening Modified: trunk/packages/aragorn/trunk/debian/watch =================================================================== --- trunk/packages/aragorn/trunk/debian/watch 2013-02-23 09:50:24 UTC (rev 13065) +++ trunk/packages/aragorn/trunk/debian/watch 2013-02-23 09:50:39 UTC (rev 13066) @@ -1,9 +1,2 @@ -# Example watch control file for uscan -# Rename this file to "watch" and then you can run the "uscan" command -# to check for upstream updates and more. -# See uscan(1) for format - -# Compulsory line, this is a version 3 file version=3 - http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn(.*).c _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit