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 switchs ignored. Composite Metazoan mitochondrial genetic code used.

-mtmam

Search for Mammalian mitochondrial tRNA genes. -i, -sr switchs 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

Dont print configuration line (which switchs 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.