ARAGORN
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ARAGORN, tRNA (and tmRNA) detection
Dean Laslett, an Australian specialist in stable RNAs, is the developer of ARAGORN.
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Upload (multi) fasta file:
or choose a genome:
Select optionsFull list of options
		  Usage:
		  aragorn -v -s -d -c -l -a -w -j -ifro<min>,<max> -t -mt -m -tv -gc -seq -br -fasta -fo -o <outfile> <filename>

		  <filename> 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. 

		  -m            Search for tmRNA genes.
		  -t            Search for tRNA genes.
                  By default, both 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. -i switch ignored. Composite
                  Metazoan mitochondrial genetic code used.
		  -mtmam        Search for Mammalian mitochondrial tRNA
                  genes. -i switch ignored. -tv switch set.
                  Mammalian mitochondrial genetic code used.
		  -mtx          Same as -mt but low scoring tRNA genes are
                  not reported.
		  -gc<num>      Use the GenBank transl_table = <num> genetic code.
		  -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.
                  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.
		  -tv           Do not search for mitochondrial TV replacement
                  loop tRNA genes. Only relevant if -mt used. 
		  -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 search for tRNA genes with minimum intron
                  length 0 bases, and only report tRNA genes with minimum
                  intron length <min> 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.
		  -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.
		  -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 with 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.
		  -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.
		  -v            Verbose. Prints out search progress
                  to STDERR.
		  -a            Print out tRNA domain for tmRNA genes
		  -o <outfile>  print output into <outfile>. If <outfile>
                  exists, it is overwritten.
                  By default, output goes to STDOUT.
		  -w            Print out genes in batch mode.
                  For tRNA genes, output is in the form:

                  Sequence name
                  N genes found
                  1 tRNA-<species> [locus 1] <Apos> (nnn)
                  i(<intron position>,<intron length>)
                  .          
                  .          
                  N tRNA-<species> [Locus N] <Apos> (nnn)
                  i(<intron position>,<intron length>)

                  N is the number of genes found
                  <species> is the tRNA iso-acceptor species
                  <Apos> is the tRNA anticodon relative position
                  (nnn) is the tRNA anticodon base triplet
                  i means the tRNA gene has a C-loop intron

                  For tmRNA genes, output is in the form:

                  n tmRNA(p) [Locus n] <tag offset>,<tag end offset>
                  <tag peptide>

                  p means the tmRNA gene is permuted
		  
		
Type
Allow introns, 0-3000 bases
Sequence topology
Strand
Output format