ARAGORN(1)

✨ NAME ✨

aragorn — the icon that sniffs out tRNA genes in nucleotide sequences 💅✨

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🎀 SYNOPSIS 🎀

aragorn [OPTION]... FILE

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💖 OPTIONS 💖

okay bestie, here's the whole menu, no skips, no gatekeeping 🫶

• -m — go hunt for tmRNA genes 🧚
• -t — go hunt for tRNA genes. by default like, everything gets detected. but the moment you say -m or -t, the other one is off unless you also ask for it 💀
• -mt — search for Metazoan mitochondrial tRNA genes. tRNA genes with introns are not detected. the -i and -sr switches get ignored. uses the composite Metazoan mitochondrial genetic code 🦋
• -mtmam — search for Mammalian mitochondrial tRNA genes. again -i and -sr are ignored, -tv gets set, and the Mammalian mitochondrial genetic code is used 🐭
• -mtx — same as -mt, except the low-scoring tRNA genes just... don't get reported 🙈
• -mtd — overlapping metazoan mitochondrial tRNA genes on opposite strands do get reported ✨
• -gc[num] — use the GenBank transl_table = [num] genetic code. you can tack on individual mods with ,BBB=<aa> where B = A,C,G, or T, and <aa> is the three letter code for an amino-acid. more than one modification is allowed, go off. e.g. -gcvert,aga=Trp,agg=Trp uses the Vertebrate Mitochondrial code and switches the codons AGA and AGG to Tryptophan 🔥
• -gcstd — use the standard genetic code 👑
• -gcmet — use the composite Metazoan mitochondrial genetic code 🌈
• -gcvert — use the Vertebrate mitochondrial genetic code 🐟
• -gcinvert — use the Invertebrate mitochondrial genetic code 🐛
• -gcyeast — use the Yeast mitochondrial genetic code 🍞
• -gcprot — use the Mold/Protozoan/Coelenterate mitochondrial genetic code 🍄
• -gcciliate — use the Ciliate genetic code 🦠
• -gcflatworm — use the Echinoderm/Flatworm mitochondrial genetic code 🪱
• -gceuplot — use the Euplotid genetic code 🌸
• -gcbact — use the Bacterial/Plant Chloroplast genetic code 🌿
• -gcaltyeast — use the alternative Yeast genetic code 🥐
• -gcascid — use the Ascidian Mitochondrial genetic code 🫧
• -gcaltflat — use the alternative Flatworm Mitochondrial genetic code 🪱✨
• -gcblep — use the Blepharisma genetic code 💫
• -gcchloroph — use the Chlorophycean Mitochondrial genetic code 🟢
• -gctrem — use the Trematode Mitochondrial genetic code 🐌
• -gcscen — use the Scenedesmus obliquus Mitochondrial genetic code 🍃
• -gcthraust — use the Thraustochytrium Mitochondrial genetic code 🫧🌊
• -tv — do not search for mitochondrial TV replacement loop tRNA genes. only relevant if you used -mt 🚫
• -c7 — only search for tRNA genes with 7 base C-loops 🌼
• -i — search for tRNA genes with introns in the anticodon loop, max length 3000 bases, min intron length 0 bases. ignored if -m is specified 😤
• -i[max] — same vibe, but the max length is [max] bases. min intron length is still 0 bases. ignored if -m is specified 🎀
• -i[min],[max] — max length [max] bases and min length [min] bases. ignored if -m is specified 💜
• -io — same as -i, but it lets tRNA genes with long introns overlap shorter tRNA genes 🤝
• -if — same as -i, but it fixes the intron between positions 37 and 38 on the C-loop (that's one base after the anticodon, iykyk) 📍
• -ifo — literally -if and -io combined, the duo 💞
• -ir — same as -i, but it reports tRNA genes with minimum length [min] bases instead of searching for tRNA genes with minimum length [min] bases. with this switch, [min] is an output filter, and the minimum intron length for searching is still 0 bases 🧐
• -c — assume each sequence is circular. the search wraps around each end. this is the default setting ⭕
• -l — assume each sequence is linear. the 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 — drop the scoring thresholds down to 95% of default levels 📉
• -ps[num] — set the scoring thresholds to [num] percent of default levels 🎚️
• -rp — flag possible pseudogenes (score < 100 or tRNA anticodon loop <> 7 bases long). heads up bestie: genes with score < 100 will not get detected or flagged if the scoring thresholds aren't also changed to below 100% (see the -ps switch) ⚠️
• -seq — print out the primary sequence 📜
• -br — show the secondary structure of the tRNA gene primary sequence using round brackets 🔵
• -fasta — print out the primary sequence in fasta format 🧬
• -fo — print out the primary sequence in fasta format only (no secondary structure) 💅
• -fon — same as -fo, but with sequence and gene numbering in the header 🔢
• -fos — same as -fo, but with no spaces in the 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 is set. the default is to allow 3 bp spacer1 and 0-2 bp spacer2, which may degrade selectivity 😬
• -v — Verbose. prints out info during the search to STDERR 🗣️
• -a — print out the tRNA domain for tmRNA genes 🧩
• -a7 — restrict the tRNA astem length to a maximum of 7 bases 🪄
• -aa — display a message if the predicted iso-acceptor species doesn't match the species in the sequence name (if it's there) 🤨
• -j — display the 4-base sequence on the 3' end of the astem regardless of the predicted amino-acyl acceptor length 👀
• -jr — allow some divergence of the 3' amino-acyl acceptor sequence from NCCA 🌀
• -jr4 — allow some divergence of the 3' amino-acyl acceptor sequence from NCCA, and display 4 bases 🌀4️⃣
• -q — do not print the configuration line (which switches and files were used) 🤫
• -rn — repeat the sequence name before the summary information 🔁
• -O [outfile] — print output to [outfile]. if [outfile] already exists, it gets overwritten. by default all output goes to stdout 📤

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🦋 DESCRIPTION 🦋

aragorn detects tRNA, mtRNA, and tmRNA genes, and it ate, no crumbs 🍽️

the bare minimum requirement is at least a 32 bit compiler architecture (the variable types int and unsigned int need to be at least 4 bytes long).

[FILE] is assumed to contain one or more sequences in FASTA format. results of the search get printed to STDOUT. all switches are optional and case-insensitive. and unless you specify -i, tRNA genes containing introns are not detected 🫢

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👑 AUTHORS 👑

Bjorn Canback <bcanback@acgt.se>, Dean Laslett <gaiaquark@gmail.com> 💖

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📚 REFERENCES 📚

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. 📖

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and that's a wrap, bestie 🎀 this lil page came from ARAGORN(1), dated 02/24/2013 — go find some genes, you absolute main character 🫶✨