-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 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.