ARWEN options and output formats
Below is the output of the -h (help) option of the standalone verison of ARWEN. The batch output format is explained at the -w flag at the bottom.
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ARWEN v1.2 Dean Laslett
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Please reference the following paper if you use this
program as part of any published research.
Laslett, D. and Canback, B. (2008) ARWEN: a
program to detect tRNA genes in metazoan mitochondrial
nucleotide sequences
Bioinformatics, 24(2); 172-175.
ARWEN detects metazoan mitochondrial tRNA genes.
Usage:
arwen -v -s -d -c -l -a -w -j -seq -mt -tv -gc -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.
-mtmam Search for Mammalian mitochondrial tRNA
genes. -tv switch set.
Mammalian mitochondrial genetic code used.
-mtx 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.
-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.
-rp Report low scoring genes as possible pseudogenes
-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).
-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.
-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.
Output is in the form:
Sequence name
N genes found
1 tRNA-<species> [locus 1] <Apos> (nnn)
.
.
N tRNA-<species> [Locus N] <Apos> (nnn)
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