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aragorn - Online in the Cloud

Run aragorn in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command aragorn that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 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
Do not 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 <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)

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