Provided by: aragorn_1.2.41-3_amd64 
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)