Provided by: aragorn_1.2.38-4_amd64 bug

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=<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.

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 <bcanback@acgt.se>, Dean Laslett <gaiaquark@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.

                                            02/24/2013                                 ARAGORN(1)