macでインフォマティクス

macでインフォマティクス

NGS関連のインフォマティクス情報についてまとめています。

tRNAやtmRNAをゲノムから素早く検出する ARAGORN

2019 2/15 Biocondaインストール追加、バッチモード追加

2019 3/10 タイトル修正

2019 5/50 インストール方法追記

 

ARAGORNは既存のtRNAとのホモロジーや二次構造などを手掛かりにゲノム中からtRNAやtmRNAを探すツール。

 

webサーバー

ARAGORN, tRNA (and tmRNA) detection

f:id:kazumaxneo:20190215121234j:plain

 

インストール

brewで導入できる。

#biocoonda
conda install -c bioconda -y ARAGORN

#homebrew
brew
install ARAGORN

 

実行方法

aragorn genome.fa -o tRNAs_output

 ポジションごとにtRNAが予測される。

f:id:kazumaxneo:20170831235702j:plain

 

 

最後にまとめが表示される。

f:id:kazumaxneo:20170831235757j:plain

例えばここで使ったゲノムではバクテリアのクロモソームから45 tRNAが見つかり、プラスミドからはtRNAは見つからなかった。tRNAのアンチコドンの頻度も表示されている。

 

genetic codeがスタンダードかどうかなどはフラグを立てて設定する。ARAGORN -hで確認できるフラグの一覧を貼っておく。

user$ ARAGORN -h

 

----------------------------

ARAGORN v1.2.36 Dean Laslett

----------------------------

 

Please reference the following papers if you use this

program as part of any published research.

 

Laslett, D. and Canback, B. (2004) ARAGORN, a

program for the detection of transfer RNA and transfer-messenger

RNA genes in nucleotide sequences

Nucleic Acids Research, 32;11-16

 

Laslett, D. and Canback, B. (2008) ARWEN: a

program to detect tRNA genes in metazoan mitochondrial

nucleotide sequences

Bioinformatics, 24(2); 172-175.

 

 

ARAGORN detects tRNA, mtRNA, and tmRNA genes.

 

Usage:

aragorn -v -s -d -c -l -a -w -j -ifro<min>,<max> -t -mt -m -tv -gc -seq -br -fasta -fo -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.

Unless -i is specified, tRNA genes containing introns

are not detected. 

 

    -m            Search for tmRNA genes.

    -t            Search for tRNA genes.

                  By default, both 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. -i switch ignored. Composite

                  Metazoan mitochondrial genetic code used.

    -mtmam        Search for Mammalian mitochondrial tRNA

                  genes. -i switch ignored. -tv switch set.

                  Mammalian mitochondrial genetic code used.

    -mtx          Same as -mt but 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. Only relevant if -mt used. 

    -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 search for tRNA genes with minimum intron

                  length 0 bases, and only report tRNA genes with minimum

                  intron length <min> 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.

    -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.

    -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 with 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.

    -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.

    -a            Print out tRNA domain for tmRNA genes

    -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.

                  For tRNA genes, output is in the form:

 

                  Sequence name

                  N genes found

                  1 tRNA-<species> [locus 1] <Apos> (nnn)

                  i(<intron position>,<intron length>)

                            .          

                            .          

                  N tRNA-<species> [Locus N] <Apos> (nnn)

                  i(<intron position>,<intron length>)

 

                  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

                  i means the tRNA gene has a C-loop intron

 

                  For tmRNA genes, output is in the form:

 

                  n tmRNA(p) [Locus n] <tag offset>,<tag end offset>

                  <tag peptide>

 

                  p means the tmRNA gene is permuted

 

 

 

リストを作るならバッチモードでランする

ARAGORN genome.fa -o output -w

>NODE_1

38 genes found

1   tRNA-Phe                c[27015,27088] 35  (gaa)

2   tRNA-Val                c[27566,27640] 35  (tac)

3   tRNA-Arg                c[41028,41100] 35  (gcg)

4   tRNA-Asn                 [46340,46415] 35  (gtt)

5   tRNA-Met                 [46592,46666] 36  (cat)

6   tRNA-Arg               [145784,145858] 35  (ccg)

7   tRNA-Arg              c[255331,255424] 35  (tcg)

8   tRNA-Tyr               [289892,289966] 35  (gta)

9   tRNA-Gln               [469893,469965] 35  (ttg)

10  tRNA-Ser               [534698,534785] 28  (gct)

11  tRNA-Ser               [585265,585349] 36  (cga)

12  tRNA-Gly              c[699904,699975] 34  (gcc)

13  tRNA-Val              c[752912,752986] 36  (gac)

14  tRNA-Val              c[802618,802696] 37  (cac)

15  tRNA-Ala               [841719,841790] 33  (ggc)

16  tRNA-Thr               [882862,882935] 35  (cgt)

17  tRNA-Gly              c[920091,920169] 38  (gcc)

18  tRNA-Arg              c[921771,921847] 37  (tcg)

19  tRNA-Thr              c[922371,922444] 35  (ggt)

20  tRNA-His              c[922446,922519] 35  (gtg)

21  tRNA-Glu              c[923590,923666] 37  (ttc)

22  tRNA-Cys              c[923671,923744] 35  (gca)

23  tRNA-Asn              c[923783,923858] 36  (gtt)

24  tRNA-Lys              c[923936,924011] 36  (ttt)

25  tRNA-Tyr              c[924144,924216] 35  (gta)

26  tRNA-Ala              c[924221,924294] 34  (cgc)

27  tRNA-Met              c[924317,924391] 37  (cat)

28  tRNA-Leu              c[924394,924476] 34  (cag)

29  tRNA-Leu              c[924509,924590] 35  (gag)

30  tRNA-Leu              c[924593,924676] 36  (taa)

31  tRNA-Trp              c[924678,924748] 33  (cca)

32  tRNA-Ser              c[924751,924838] 38  (gga)

33  tRNA-Ser              c[924839,924922] 36  (tga)

34  tRNA-Ser              c[924957,925046] 36  (gct)

35  tRNA-Pro              c[925049,925121] 35  (tgg)

36  tRNA-Asp              c[925322,925396] 36  (gtc)

37  tRNA-Gln              c[925408,925483] 37  (ttg)

38  tRNA-Arg              c[927017,927091] 36  (tcg)

 

 

引用

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

Dean Laslett Bjorn Canback

Nucleic Acids Research, Volume 32, Issue 1, 1 January 2004, Pages 11–16,