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ktrnascan_se |
Function
Finds tRNA genes using tRNAscan-SEDescription
ktrnascan_se detects transfer RNA genes in DNA sequence utilizing tRNAscan-SE. tRNAscan-SE identifies 99–100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.ktrnascan_se utilizes tRNAscan-SE server provided by Lowe Lab. Original web-service is located at the following URL:
http://lowelab.ucsc.edu/tRNAscan-SE/
This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. ktrnascan_se is thus an interface of "runtRNAscan" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://soap.g-language.org/kbws/ for more information.
Usage
Here is a sample session with ktrnascan_se
% ktrnascan_se
Finds tRNA genes using tRNAscan-SE
Input (gapped) sequence(s): refseq:NC_000908
Output file [nc_000908.ktrnascan_se]:
Jobid: kbws_4760102
*****
tRNAscan-SE v.1.21 (Oct 2000) - scan sequences for transfer RNAs
Please cite:
Lowe, T.M. & Eddy, S.R. (1997) "tRNAscan-SE: A program for
improved detection of transfer RNA genes in genomic sequence"
Nucl. Acids Res. 25: 955-964.
This program uses a modified, optimized version of tRNAscan v1.3
(Fichant & Burks, J. Mol. Biol. 1991, 220: 659-671),
a new implementation of a multistep weight matrix algorithm
for identification of eukaryotic tRNA promoter regions
(Pavesi et al., Nucl. Acids Res. 1994, 22: 1247-1256),
as well as the RNA covariance analysis package Cove v.2.4.2
(Eddy & Durbin, Nucl. Acids Res. 1994, 22: 2079-2088).
Cove-predicted tRNA secondary structures rendered by
NAVIEW (c) 1988 Robert E. Bruccoleri.
Results
Sequence Your-seq
Subsequence Your-seq.t1 257160 257233
Sequence Your-seq.t1
Source Your-seq
Brief_identification tRNA-Cys
Transcript tRNA "TGC Cys C"
Score tRNAscan-SE-1.21 56.59
Sequence Your-seq
Subsequence Your-seq.t2 257271 257344
Sequence Your-seq.t2
Source Your-seq
Brief_identification tRNA-Pro
Transcript tRNA "CCA Pro P"
Score tRNAscan-SE-1.21 79.30
Sequence Your-seq
Subsequence Your-seq.t3 257351 257424
Sequence Your-seq.t3
Source Your-seq
Brief_identification tRNA-Met
Transcript tRNA "ATG Met M"
Score tRNAscan-SE-1.21 76.46
Sequence Your-seq
Subsequence Your-seq.t4 257447 257520
Sequence Your-seq.t4
Source Your-seq
Brief_identification tRNA-Met
Transcript tRNA "ATG Met M"
Score tRNAscan-SE-1.21 75.25
Sequence Your-seq
Subsequence Your-seq.t5 257561 257649
Sequence Your-seq.t5
Source Your-seq
Brief_identification tRNA-Ser
Transcript tRNA "TCA Ser S"
Score tRNAscan-SE-1.21 59.71
Sequence Your-seq
Subsequence Your-seq.t6 257666 257739
Sequence Your-seq.t6
Source Your-seq
Brief_identification tRNA-Met
Transcript tRNA "ATG Met M"
Score tRNAscan-SE-1.21 71.85
Sequence Your-seq
Subsequence Your-seq.t7 257744 257814
Sequence Your-seq.t7
Source Your-seq
Brief_identification tRNA-Asp
Transcript tRNA "GAC Asp D"
Score tRNAscan-SE-1.21 58.26
Sequence Your-seq
Subsequence Your-seq.t8 257820 257892
Sequence Your-seq.t8
Source Your-seq
Brief_identification tRNA-Phe
Transcript tRNA "TTC Phe F"
Score tRNAscan-SE-1.21 74.07
Sequence Your-seq
Subsequence Your-seq.t9 266425 266498
Sequence Your-seq.t9
Source Your-seq
Brief_identification tRNA-Arg
Transcript tRNA "CGC Arg R"
Score tRNAscan-SE-1.21 67.11
Sequence Your-seq
Subsequence Your-seq.t10 306619 306690
Sequence Your-seq.t10
Source Your-seq
Brief_identification tRNA-Arg
Transcript tRNA "AGG Arg R"
Score tRNAscan-SE-1.21 56.90
Run Statistics:
Started: Mon Jan 4 23:05:56 PST 2010
------------------------------------------------------------
Search Mode: General
Searching with: tRNAscan + EufindtRNA -> Cove
Covariance model: TRNA2.cm
tRNAscan parameters: Strict
EufindtRNA parameters: Relaxed (Int Cutoff= -32.1)
Pseudogene checking disabled
Reporting HMM/2' structure score breakdown
------------------------------------------------------------
First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read: 1
Seqs w/at least 1 hit: 1
Bases read: 580078 (x2 for both strands)
Bases in tRNAs: 3088
tRNAs predicted: 39
Av. tRNA length: 79
Script CPU time: 0.08 s
Scan CPU time: 0.39 s
Scan speed: 2974.8 Kbp/sec
First pass search(es) ended: Mon Jan 4 23:05:57 PST 2010
Cove Stats:
-----------
Candidate tRNAs read: 39
Cove-confirmed tRNAs: 36
Bases scanned by covels: 3634
% seq scanned by covels: 0.3 %
Script CPU time: 0.09 s
Cove CPU time: 5.84 s
Scan speed: 622.3 bp/sec
Cove analysis of tRNAs ended: Mon Jan 4 23:06:03 PST 2010
Summary
--------
Overall scan speed: 181274.4 bp/sec
tRNAs decoding Standard 20 AA: 35
Selenocysteine tRNAs (TCA): 1
Possible suppressor tRNAs (CTA,TTA): 0
tRNAs with undetermined/unknown isotypes: 0
Predicted pseudogenes: 0
-------
Total tRNAs: 36
tRNAs with introns: 0
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Isotype / Anticodon Counts:
Ala : 1 AGC: GGC: CGC: TGC:
Gly : 2 ACC: GCC: CCC: TCC:
Pro : 1 AGG: GGG: CGG: TGG:
Thr : 3 AGT: GGT: CGT: TGT:
Val : 1 AAC: GAC: CAC: TAC:
Ser : 4 AGA: GGA: CGA: TGA: ACT: GCT:
Arg : 4 ACG: GCG: CCG: TCG: CCT: TCT:
Leu : 4 AAG: GAG: CAG: TAG: CAA: TAA:
Phe : 1 AAA: GAA:
Asn : 1 ATT: GTT:
Lys : 2 CTT: TTT:
Asp : 1 ATC: GTC:
Glu : 1 CTC: TTC:
His : 1 ATG: GTG:
Gln : 1 CTG: TTG:
Ile : 1 AAT: GAT: TAT:
Met : 3 CAT:
Tyr : 1 ATA: GTA:
Supres: 0 CTA: TTA:
Cys : 1 ACA: GCA:
Trp : 1 CCA:
SelCys: 1 TCA:
Predicted tRNA Secondary Structures:
Your-seq.trna1 (257160-257233) Length: 74 bp
Type: Cys Codon: TGC at 36-38 (257195-257197) Score: 56.59
HMM Sc=22.52 Sec struct Sc=34.07
* | * | * | * | * | * | * |
Seq: GGTGCCTTAGCCAAGTGGActcAAGGCCTGGAGCTGCAACCTCCATAtCGTCAGTTCGAATCTGACAGGCACCT
Str: >>>>>>>..>>>............>>>>.......>>>>.......<<<<<<<<<<<<.
Your-seq.trna2 (257271-257344) Length: 74 bp
Type: Pro Codon: CCA at 35-37 (257305-257307) Score: 79.30
HMM Sc=55.47 Sec struct Sc=23.83
* | * | * | * | * | * | * |
Seq: CGGGAAGTAGCTTAGTTtGGTAGAGCACTTGGTTTGGGACCAAGGGGtCGCAGGTTCAAATCCTGTCTTCCCGA
Str: >>>>>>>..>>>>.........>>>>.......>>>>.......<<<<<<<<<<<<.
Your-seq.trna3 (257351-257424) Length: 74 bp
Type: Met Codon: ATG at 35-37 (257385-257387) Score: 76.46
HMM Sc=43.95 Sec struct Sc=32.51
* | * | * | * | * | * | * |
Seq: GGCTGGATACCTCAGTTGGTtAGAGGGCCCGGTTCATACCCGGGTTGtCGTGAGTTCGAGTCTCACTCCAGCCA
Str: >>>>>>>..>>>>.........>>>>.......>>>>.......<<<<<<<<<<<<.
Your-seq.trna4 (257447-257520) Length: 74 bp
Type: Met Codon: ATG at 35-37 (257481-257483) Score: 75.25
HMM Sc=53.91 Sec struct Sc=21.34
* | * | * | * | * | * | * |
Seq: GGATCTATAGCTCAATTGGTtAGAGCCCCCGACTCATAATCGGTCTGtTACAGGTTCAAGTCCTGTTAGATCCA
Str: >>>>>>>..>>>>.........>>>.......>>>>.......<<<<<<<<<<<<.
Your-seq.trna5 (257561-257649) Length: 89 bp
Type: Ser Codon: TCA at 35-37 (257595-257597) Score: 59.71
HMM Sc=24.23 Sec struct Sc=35.48
* | * | * | * | * | * | * | * | *
Seq: GGAGACTTACCCAAGCGGCtgAAGGGTTCGGTCTTGAAAACCGAGAgGTGCTTTATAAGCACGCGAGGGTTCGAATCCCTCAGTCTCCG
Str: >>>>>>>..>>>...........>>>>.......>>>>>...>>>>.......<<<<<<<<<<<<.
Your-seq.trna6 (257666-257739) Length: 74 bp
Type: Met Codon: ATG at 35-37 (257700-257702) Score: 71.85
HMM Sc=46.39 Sec struct Sc=25.46
* | * | * | * | * | * | * |
Seq: CGCGGGATAGAGCAGTTGGTcAGCTCGTCAGGCTCATAATCTGAAGGtCGAGGGTTCAAATCCCTCTCCCGCAA
Str: .>>>>>>..>>>>.........>>>>.......>>>>.......<<<<<<<<<<<..
Your-seq.trna7 (257744-257814) Length: 71 bp
Type: Asp Codon: GAC at 33-35 (257776-257778) Score: 58.26
HMM Sc=34.50 Sec struct Sc=23.76
* | * | * | * | * | * | * |
Seq: GGTTCCATGGTGTAGTGATAACATATCTCCCTGTCACGGAGGGGtTGCGGGTTTGATTCCCGTTGGAACCG
Str: >>>>>>>..>>>>.......>>>>.......>>>>.......<<<<<<<<<<<<.
Your-seq.trna8 (257820-257892) Length: 73 bp
Type: Phe Codon: TTC at 34-36 (257853-257855) Score: 74.07
HMM Sc=46.53 Sec struct Sc=27.54
* | * | * | * | * | * | * |
Seq: GGTCTTGTAGCTCAGTCGGTAGAGCAACGGTCTGAAGAACCGTGTGtCGGCAGTTCGATTCTGCCCGAGACCA
Str: >>>>>>>..>>>>........>>>>.......>>>>.......<<<<<<<<<<<<.
Your-seq.trna9 (266425-266498) Length: 74 bp
Type: Arg Codon: CGC at 35-37 (266459-266461) Score: 67.11
HMM Sc=43.38 Sec struct Sc=23.73
* | * | * | * | * | * | * |
Seq: GTCATCATAGCTCAATAGGAcAGAGTATCAGCTTGCGGAGCTGAGGGtTACAGGTTCGATTCCTGTTGGTGACG
Str: >>>>>>>..>>>>.........>>>>.......>>>>.......<<<<<<<<<<<<.
Your-seq.trna10 (306619-306690) Length: 72 bp
Type: Arg Codon: AGG at 34-36 (306652-306654) Score: 56.90
HMM Sc=22.17 Sec struct Sc=34.73
* | * | * | * | * | * | * |
Seq: CTTCCCTTGGTGCAATGGAcAGCACAACTGAGTCCTAATCAGTAAATAGAGGTTCAACTCCTCTAGGGAAGG
Str: >>>>>>>..>>>>........>>>>.......>>>>.......<<<<<<<<<<<<.
Candidate tRNAs not verified by Cove analysis:
>Your-seq.t1 (Fp Hit: 199996-200090, 95 bp, Src: Eu)
ATCACCTTACCCTTTGCTTTAGTGCAAGCATTTGCTGTGATCCAAATTGCTACTAATGCA
GGCACTGGTTCAAGTCCGATTAGTTTAGCTAATAG
>Your-seq.t2 (Fp Hit: 222067-222172, 106 bp, Src: Eu)
CCTTTTAAAGGCTTTGGTTTAACTGGTAATGCCCCTACTGATTGGAATGAGATCAAAGGT
AAAGTTCCAGTAGAAGTAGTTCAATCCCCCCATTCCCCCAACCTCT
>Your-seq.t36 (Fp Hit: 99482-99280, 203 bp, Src: Eu)
TTTTTTAACAATGCTACTGTAGTTGGTAAAGCAATTGCAGTAGTACCAAAAGCACCAGAT
ATTGACAAGCAGATAGTAGTTATTGTACTTAATTTCATATGTTAAGAGAAAAGTTATGAA
TTTATAAAGAGAGCAAACTTAAACAGCCAATAAGGATCTTATTAGTTGTTGATAAGTTCA
AATCAAAAGGTTTTATCTCTAAA
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Command line arguments
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-seqall] (Parameter 1) |
seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | 2 |
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.ktrnascan_se |
| Additional (Optional) qualifiers | ||||
| -title | string | title of your job | Any string | |
| -mode | string | search mode | Any string | Default |
| -source | string | training data set | Any string | Mixed (general tRNA model) |
| -gcode | string | Genetic Code for tRNA Isotype Prediction | Any string | |
| -pesudogene | boolean | Disable pseudo gene checking | Boolean value Yes/No | No |
| -origin | boolean | Show origin of first-pass hits | Boolean value Yes/No | No |
| -ace | boolean | Display results in ACeDB format | Boolean value Yes/No | No |
| -codons | boolean | Show codons instead of tRNA anticodons | Boolean value Yes/No | No |
| -fpos | boolean | Show false positives from tRNAscan/EufindtRNA | Boolean value Yes/No | No |
| -breakdown | boolean | Show primary and secondary structure components to Cove scores | Boolean value Yes/No | No |
| -covescore | string | Cove score cutoff | Any string | |
| -euparams | string | EufindtRNA search parameters | Any string | Default |
| -euscore | string | Intermediate score cutoff | Any string | |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
Input file format
ktrnascan-se can use any genome sequence data that seqret can read.Output file format
The output from ktrnascan_se is general output format of tRNAscan-SE.Data files
None.Notes
None.References
Lowe, T.M., and Eddy, S.R., tRNAscan-SE: a program for improved detection
of transfer RNA genes in genomic sequence, Nucleic Acids Research, 25, 955-964.
Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with a status of 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| seqret | Reads and writes (returns) sequences |