Specifiy this option to write results to file rather than standard output.
This option saves results and secondary structure information (as predicted by the coves program) in file. Use ``$'' in place of file to send to standard output. An example of the output format for one tRNA appears below:
CELF22B7.trna4 (26992-26920) Length: 73 bp
Type: Phe Anticodon: GAA at 34-36 (26959-26957) Score: 73.88
* | * | * | * | * | * | * |
Seq: GCCTCGATAGCTCAGTTGGGAGAGCGTACGACTGAAGATCGTAAGGtCACCAGTTCGATCCTGGTTCGGGGCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<.
| | | | | | | || |
+-----+ +--------------+ +---------------+ +---------------++-----+
| D-stem/loop Anticodon TPC stem/loop |
| stem/loop |
+----------------------------------------------------------------+
Isoacceptor stem
The first line contains the sequence name, trna#, tRNA bounds (in
parentheses), and length of the tRNA. The next line contains the
isoacceptor tRNA Type, Anticodon (with tRNA-relative and
sequence-absolute bounds), and the Cove Score. This is identical
information as would be seen in the tabular output format, excluding
the anticodon bounds. The next line contains hash marks every 5 and
10 bp to ease position identification in the tRNA sequence that
appears on the following line. On the sequence line, nucleotides
matching the ``consensus'' tRNA model used in Cove analysis appear in
upper case, while introns and other nucleotides in non-conserved
positions are printed in lower-case letters. The last line contains
predicted secondary structure folding of the tRNA, with nested
'>' and '<' symbols representing base pairings. The
various tRNA features are labelled in this example.
This option allows results to be written in ACeDB format instead of the default tabular output format.
This option directs tRNAscan-SE to write a brief summary to file
which contains the run options selected as well as statistics on the
number of tRNAs detected at each phase of the search, search speed,
and other statistics (examples on following pages).
Following is a description of each of these statistics, followed by an example stats summary file created from scanning the C. elegans cosmid F59C12:
tRNAscan-SE run results (on host <computer name>)
Started: <time & date tRNAscan-SE began>
<Parameters used for search printed here>
First-pass (tRNAscan/EufindtRNA) Stats:
---------------------------------------
Sequences read: <total # of FASTA sequences read>
Seqs w/at least 1 hit: <total sequences with at least one tRNA predicted>
Bases read: <total nucleotides in all sequences searched (both strands)>
Bases in tRNAs: <total nucleotides in tRNAs predicted>
tRNAs predicted: <# tRNAs predicted from first-pass search program(s)>
Av. tRNA length: <average tRNA length>
Script CPU time: <CPU time spent by tRNAscan-SE
reading seqs, setting up run & writing results>
Scan CPU time: <CPU time spent by tRNAscan/EufindtRNA finding tRNAs>
Scan speed: <Averaged tRNAscan+EufindtRNA search speed>
First pass search(es) ended: <time & date tRNAscan/EufindtRNA searches
finished, Cove analysis begins>
Cove Stats:
-----------
Candidate tRNAs read: <number of tRNAs detected by tRNAscan/EufindtRNA
that were passed to Cove for verification>
Cove-confirmed tRNAs: <number of tRNAs positively confirmed by Cove>
Bases scanned by covels: <total nucleotides in all tRNAs searched by
Cove (covels-SE program) analysis>
% seq scanned by covels: <percent of total nucleotides in input
sequences that were analyzed by Cove>
Script CPU time: <CPU time spent by tRNAscan-SE reading
seqs, setting up runs & writing results>
Cove CPU time: <CPU time spent by Cove analysis programs>
Scan speed: <Average Cove search speed>
Cove analysis of tRNAs ended: <time & date Cove analysis
and tRNAscan-SE completed>
Summary
--------
Confirmed tRNAs: <total tRNAs predicted by tRNAscan-SE>
Overall scan speed: <Average search speed for tRNAscan-SE>
An example stats summary file using the default search options on cosmid F59C12 follows:
tRNAscan-SE run results (on host wol) Started: Wed Feb 5 15:02:30 CST 1997 ------------------------------------------------------------ Sequence file(s) to search: F59C12.fa Results written to: Standard output Output format: Tabular Searching with: tRNAscan + EufindtRNA -> Cove tRNAscan parameters: Strict EufindtRNA parameters: Relaxed (Int Cutoff= -32.1) Search statistics saved in: F59C12.stats ------------------------------------------------------------ First-pass (tRNAscan/EufindtRNA) Stats: --------------- Sequences read: 1 Seqs w/at least 1 hit: 1 Bases read: 57976 (both strands) Bases in tRNAs: 299 tRNAs predicted: 4 Av. tRNA length: 74 Script CPU time: 0.19 s Scan CPU time: 0.55 s Scan speed: 105.4 Kbp/sec First pass search(es) ended: Wed Feb 5 15:02:31 CST 1997 Cove Stats: ----------- Candidate tRNAs read: 4 Cove-confirmed tRNAs: 3 Bases scanned by covels: 355 % seq scanned by covels: 0.6 % Script CPU time: 0.24 s Cove CPU time: 8.08 s Scan speed: 43.9 bp/sec Cove analysis of tRNAs ended: Wed Feb 5 15:02:43 CST 1997 Summary -------- Confirmed tRNAs: 3 Overall scan speed: 6399.1 bp/sec
This option directs the program to print messages indicating the progress of the program to standard output. If final results are also being sent to standard output, some of these messages will be suppressed so as to not interrupt display of the results.
Identical to -d option, but sends message to file instead of
standard output.
Note: the -d option overrides the -l option if both are
specified on the same command line.
This option suppresses the program credits and run option selections normally printed to standard error at the beginning of each run.
This option eliminates column headers that appear by default when writing results in tabular output format. Useful if results are to be parsed or sent to another program.
This option causes tRNAscan-SE to output a tRNA's corresponding codon in place of its anticodon.
The '#' symbol may be used as shorthand to specify ``default'' file
names for output files. The default file names are constructed by
using the input sequence file name, followed by an extension
specifying the output file type seqfile.ext where
.ext is:
Note:
This option allows the user to specify the default output file prefix when using the '#' file name specification (instead of using the input sequence file name).
This option displays which of the first-pass scanners detected the tRNA being output. ``Ts'', ``Eu'', or ``Bo'' will appear in the last column of Tabular output, indicating that either tRNAscan 1.4, EufindtRNA, or both scanners detected the tRNA, respectively.