介绍
tRNAscan-SE: An improved tool for transfer RNA detection
tRNAscan-SE was written in the PERL (version 5) script language.
Input consists of DNA or RNA sequences in FASTA format. tRNA
predictions are output in standard tabular or ACeDB format.
tRNAscan-SE does no tRNA detection itself, but instead combines the
strengths of three independent tRNA prediction programs by negotiating
the flow of information between them, performing a limited amount of
post-processing, and outputting the results in one of several
formats.
输入
序列文件：
fasta格式，例如
>seqname1
AAAAAAAAGCTACTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTC
类型:
-E : search for eukaryotic tRNAs (default)
-B : search for bacterial tRNAs
-A : search for archaeal tRNAs
-M <span><</span>model> : search for mitochondrial tRNAs
options: mammal, vert
-O : search for other organellar tRNAs
结果
1. trna汇总表
out.gff
例如
Sequence tRNA Bounds tRNA Anti Intron Bounds Cove
Name tRNA # Begin End Type Codon Begin End Score Note
-------- ------ ----- ------ ---- ----- ----- ---- ------ ------
tig00000462_pilon_pilon 1 1742900 1742984 Leu GAG 0 0 57.02
tig00000462_pilon_pilon 2 2139254 2139329 Leu CAA 0 0 51.89
tig00000462_pilon_pilon 3 2955236 2955309 Gly TCC 0 0 81.79
tig00000462_pilon_pilon 4 3034584 3034656 Arg TCT 0 0 78.55
2. tRNA结构文件
out.tRNA.struc
例如
tig00000462_pilon_pilon.trna1 (1742900-1742984) Length: 85 bp
Type: Leu Anticodon: GAG at 34-36 (1742933-1742935) Score: 57.02
* | * | * | * | * | * | * | * |
Seq: GTCCGGGTGGCGGAATGGCaGACGCGCTAGCTTGAGGTGCTAGTGCCCTTTATCGGGCGTGGGGGTTCAAGTCCCCCCTCGGACA
Str: >>>>>>>..>>>..........<span><</span><span><</span><span><</span>.>>>>>.......<span><</span><span><</span><span><</span><span><</span><span><</span>.>>>>......<span><</span><span><</span><span><</span><span><</span>..>>>>>.......<span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span>.
3. trna序列文件
trna.fasta
例如
>tig00000462_pilon_pilon.trna1 tig00000462_pilon_pilon:1742900-1742984 (+) Leu (GAG) 85 bp Sc: 57.02
GTCCGGGTGGCGGAATGGCAGACGCGCTAGCTTGAGGTGCTAGTGCCCTTTATCGGGCGT
GGGGGTTCAAGTCCCCCCTCGGACA
