Björn Canbäck Bioinformatics

ARWEN, tRNA detection in metazoan mitochondrial sequences

Dean Laslett, an Australian specialist in stable RNAs, is the developer of ARWEN. There is a version for download which requires compilation with a C-compiler (for example gcc -o arwen arwen1.2.3.c: ignore any warnings about trigraphs.). Test results from a comparison between tRNAscan-SE and ARWEN are found here.

Input sequence (both strands will be searched, max. 15 MB)

Upload a fasta file with one or several sequences:

Select options (see here for all options in the standalone version)

Search for mammalian mitochondrial tRNA genes (-mtmam) (the -tv switch below is set by this option)
Do not search for mitochondrial TV replacement loop tRNA genes (-tv)
Don't report low scoring tRNA genes (-mtx)
Use mammalian mitochondrial genetic code (-gcmam) (default is a composite metazoan mitochondrial code)
Print out primary sequence (-seq)
Batch output (-w) (default is standard which includes the secondary structure)

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Notes

The input sequence will be searched in both directions and it is assumed that it has a circular topology.

Cite

Please reference the following paper if you use the program as part of any published research:

• Laslett, D. & Canbäck B. (2008) ARWEN, a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24;172-175. PMID: 18033792

Revision history

Version 1.2, January 1st, 2008

• The first public version

Credits

• ARWEN is written in C by Dean Laslett.
• This online version was created by Björn Canbäck
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Last modified: September 8, 2009