ARWEN protocols

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ARWEN specifications

Information


Unique identifier OMICS_04228
Name ARWEN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_04228
Name ARWEN
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for ARWEN

ARWEN in pipelines

 (10)
2018
PMCID: 5906601
PMID: 29670192
DOI: 10.1038/s41598-018-24382-3

[…] mapping and short read post-processing was performed using bowtie2 software and samtools utilities, respectively. the prediction of protein-coding genes, rrnas and trnas was done using mitos and arwen software and validated manually by comparing homologous regions with a loa loa mitochondria reference in artemis. a mitogenome map was generated using the brig software package., a provisional […]

2018
PMCID: 5931646
PMID: 29718949
DOI: 10.1371/journal.pone.0196466

[…] coding genes were annotated by using ncbi orf finder (https://www.ncbi.nlm.nih.gov/orffinder/) and blastx with the invertebrate mitochondrial code. the positions of trna genes were determined by arwen v.1.2 [] and mitos web server []; and secondary structures of trnas were inferred using mitos in default search mode. the rrna genes were identified by blast searches […]

2017
PMCID: 5219674
PMID: 28061879
DOI: 10.1186/s13071-016-1956-9

[…] annotated using trna scan-se v.1.21 (http://lowelab.ucsc.edu/trna scan -se) with search mode = “eufind trna- cove”, genetic code = “invertebrate mito”, and cove score cut-off = 0.1, and the software arwen (http://130.235.46.10/arwen/) []. the map of the species was visualized using the genome vx online tool (http://wolfe.ucd.ie/genomevx/) []. repeat sequences were found using spectral repeat […]

2017
PMCID: 5446695
PMID: 28549457
DOI: 10.1186/s12864-017-3807-2

[…] eluted in nuclease-free water or buffer ae. pcrs were done with 15-170 ng of extracted dna in 50 μl tubes, with varying conditions., for gene annotation, blast searches [], as well as mitos [], arwen [] and dogma [] predictions were employed. for the analysis of putative atp8 sequences, we also used smart [] with default parameters to identify domains, and the expasy tool protscale […]

2017
PMCID: 5571815
PMID: 28848689
DOI: 10.7717/peerj.3692

[…] start codon (atg, ata, or atc) downstream of the preceding gene, and ending with the first stop codon in frame (taa or tag). trna genes and their structure were identified with mitos () and arwen (). secondary structures were predicted using the rnafold server, included in the viennarna web services (http://rna.tbi.univie.ac.at/; ); the folding temperature was set at 16 °c […]


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ARWEN in publications

 (49)
PMCID: 5931646
PMID: 29718949
DOI: 10.1371/journal.pone.0196466

[…] coding genes were annotated by using ncbi orf finder (https://www.ncbi.nlm.nih.gov/orffinder/) and blastx with the invertebrate mitochondrial code. the positions of trna genes were determined by arwen v.1.2 [] and mitos web server []; and secondary structures of trnas were inferred using mitos in default search mode. the rrna genes were identified by blast searches […]

PMCID: 5916287
PMID: 29721275
DOI: 10.1002/ece3.3918

[…] annotations were performed using the mitochondrial genome annotation server mitos (bernt et al., ) with default parameters. additional search and validation of trna sequences were performed using arwen (laslett & canbäck, ) and trnascan‐se (lowe & eddy, ; schattner, brooks, & lowe, ). automated annotation was confirmed and edited manually by comparison with published anuran […]

PMCID: 5706379
PMID: 29183283
DOI: 10.1186/s12862-017-1086-9

[…] mitochondrial protein coding genes were annotated by identifying open reading frames (orf) in geneious and blastp to confirm orf identification and protein length. trna genes were identified using arwen []. the two rrna genes were identified by blastn search of genbank []. dnasp [] was used to assess the magnitude selective pressure by dn/ds rations for all protein coding genes., […]

PMCID: 5651803
PMID: 29057900
DOI: 10.1038/s41598-017-13807-0

[…] exception of the trnm with c at the wobble position. surprisingly, two copies of trnl2, both with taa anticodon were found. they both should form typical, stable cloverleaf structures according to arwen, with comparable bitscores (30 and 31). one of the genes was located between nd2 and nd4, in the first contig, while the alternative version was present between cox2 and nd3 in the second […]

PMCID: 5578989
PMID: 28860662
DOI: 10.1038/s41598-017-10713-3

[…] calculated in a consensus tree. the result was showed using figtree v.1.4.2., the trna genes of acp mitogenome were predicted by their cloverleaf secondary structure using trnascan-se v.1.21 and arwen v.1.2, . the variations in all trna genes among mt-capsy, mt-gdpsy, mt-flpsy and mt-flpsy-fp were detected by alignment using clustal w. snps or gaps were identified and verified by additional […]


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ARWEN institution(s)
Murdoch University, Perth, Western Australia, Australia; Björn Canbäck Bioinformatik, Rydebäck, Sweden

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No longer available online as of Feb 2018