NAME
aragorn - detect tRNA genes in nucleotide sequencesSYNOPSIS
aragorn [OPTION]... FILEOPTIONS
-mSearch 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).AUTHORS
Bjorn Canback <[email protected]>, Dean Laslett <[email protected]>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| 02/24/2013 |