Provided by: aragorn_1.2.38-2_amd64
aragorn - detect tRNA genes in nucleotide sequences
aragorn [OPTION]... FILE
-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 switches ignored. Composite Metazoan mitochondrial genetic code used. -mtmam Search for Mammalian mitochondrial tRNA genes. -i, -sr switches 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. 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. -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. -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. -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 Do not print configuration line (which switches and files were used). -rn Repeat sequence name before summary information. -O [outfile] Print output to . If ['outfile] already exists, it is overwritten. By default all output goes to stdout.
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). [FILE] 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.
Bjorn Canback <email@example.com>, Dean Laslett <firstname.lastname@example.org>
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. 02/24/2013 ARAGORN(1)