---------------------------- ARAGORN v1.2.40 Dean Laslett ---------------------------- Please reference the following papers if you use this program as part of any published research. 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. ARAGORN detects tRNA, mtRNA, and tmRNA genes. Usage: aragorn -v -e -s -d -c -l -j -a -q -rn -w -ifro, -t -mt -m -rp -ps -gc -tv -seq -br -fasta -fo -o is assumed to contain one or more sequences in FASTA or GENBANK 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. -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 switch 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 Use the GenBank transl_table = 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. -gcptero Use Pterobranchia mitochondrial genetic code. -gcgrac Use Gracilibacteria genetic code. -gcpach Use Pachysolen tannophilus genetic code. -gckary Use Karyorelict genetic code. -gccond Use Condylostoma genetic code. -gcmeso Use Mesodinium genetic code. -gcperi Use Peritrich genetic code. -gcblast Use Blastocrithidia genetic code. -gcceph Use Cephalodiscidae mitochondrial UAA-Tyr 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. -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. -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 Search for tRNA genes with introns in anticodon loop with maximum length bases. Minimum intron length is 0 bases. Ignored if -m is specified. -i, Search for tRNA genes with introns in anticodon loop with maximum length bases, and minimum length 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 bases rather than search for tRNA genes with minimum length bases. With this switch, acts as an output filter, minimum intron length for searching is still 0 bases. -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. -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. -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. -e Print out score for each reported gene. -ps Lower scoring thresholds to 95% of default levels. -ps Change scoring thresholds to 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). -rp Flag possible pseudogenes and change score threshold to percent of default levels. -seq Print out primary sequence. -br Show secondary structure of tRNA gene primary sequence, or tRNA domain for tmRNA genes, using round brackets. -svg Generate SVG image file code for secondary structure. -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. -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). -amt Change annotated tRNA length mismatch reporting threshold to bases when searching GENBANK files. Default is 10 bases. -amm Change annotated tmRNA length mismatch reporting threshold to bases when searching GENBANK files. Default is 30 bases. -q Dont print configuration line (which switches and files were used). -rn Repeat sequence name before summary information. -o Print output to . If already exists, it is overwritten. By default all output goes to stdout. -w Print out in batch mode. -wa Same as -w, but for 6 or 8 base anticodon loops, print possible iso-acceptor species as ?(|) instead of ??? For tRNA genes, batch mode output is in the form: Sequence name N genes found 1 tRNA- [locus 1] (nnn) i(,) . . N tRNA- [Locus N] (nnn) i(,) N is the number of genes found is the tRNA iso-acceptor species is the tRNA anticodon relative position (nnn) is the tRNA anticodon base triplet i means the tRNA gene has a C-loop intron For tmRNA genes, output is in the form: n tmRNA(p) [Locus n] , p means the tmRNA gene is permuted -wunix Get around problem with some windows gcc compilers (found so far in Strawberry Perl and Active Perl) when reading Unix files. Execution speed may be slower for large files. Execution speed will be a lot slower for files with many small sequences.