--- name: "aragorn" section: "1" platform: "linux" package: "aragorn" version: "1.2.41-3" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/aragorn" --- # aragorn(1) detect tRNA genes in nucleotide sequences ## NAME aragorn - detect tRNA genes in nucleotide sequences ## SYNOPSIS **aragorn** \[*OPTION*\]... *FILE* ## 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** 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*=\ B = A,C,G, or T. \ 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. ## 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). \[*FILE*\] 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. ## AUTHORS Bjorn Canback \, Dean Laslett \ ## 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.