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SPLITS specifications

Information


Unique identifier OMICS_23948
Name SPLITS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Maintained No

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Publication for SPLITS

SPLITS citations

 (15)
call_split

The RNA splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity

2018
Nucleic Acids Res
PMCID: 5829648
PMID: 29346615
DOI: 10.1093/nar/gky003
call_split See protocol

[…] N21, using tRNAscan-SE 2.0 with a setting of source ‘Archaeal’ and search mode ‘Default’ (). tRNA gene candidates predicted with irregular loop or stem size were further subjected to BHB search using SPLITS, with the given parameters –p ‘0.5’ –f ‘’−5’ –h ‘4’ () to predict correct intron sequences. […]

library_books

Phylogeny and biogeography of the remarkable genus Bondarzewia (Basidiomycota, Russulales)

2016
Sci Rep
PMCID: 5041112
PMID: 27680391
DOI: 10.1038/srep34568

[…] Several studies have attempted to date the evolutionary splits of fungi using various calibration strategies. Here, we used internal calibration to determine the divergence time between Ascomycota and Basidiomycota, 582 Mya, with the 400-million-years-old […]

library_books

Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

2016
PMCID: 4880095
PMID: 27191589
DOI: 10.3201/eid2206.151565

[…] from the admixture values using the Clustering Markov Packager Across K (CLUMPAK) (http://www.clumpak.tau.ac.il) and built final plots with STRUCTURE PLOT (,).We also inferred Coccidioides population splits and mixtures trees using a statistical model related to common ancestors through a graph of ancestral populations via TreeMix software (Pritchard Laboratory) (). In brief, we inferred a populat […]

call_split

Nucleomorph Genome Sequences of Two Chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata

2015
Genome Biol Evol
PMCID: 4494063
PMID: 26002880
DOI: 10.1093/gbe/evv096
call_split See protocol

[…] orphan genes (ORFans). rRNAs were identified using RNAmmer 1.2 () and BLASTn against rRNA sequences of B. natans. Transfer RNAs (tRNAs) and permuted tRNAs were predicted by tRNAscan-SE v. 2.1 () and SPLITS (), and the following parameters were applied: -c -p 0.55 -F -3 -h -3 () and -c -p 0.6 -F -1 (). Small nuclear RNAs (snRNAs) were detected using fRNAdb with an option (word size = 7) (). Simple […]

library_books

Handling tRNA introns, archaeal way and eukaryotic way

2014
Front Genet
PMCID: 4090602
PMID: 25071838
DOI: 10.3389/fgene.2014.00213

[…] joined from the 1–25 fragment common for the two, either one of the two specific fragments covering 26–37 with the anticodons, and the 3′-half used for all of the three tRNA-Gly isodecoders. Most of splits in the separated tRNA genes are located at canonical position (37/38) while those are at position 29/30 of tRNA-AlaCGC and tRNA-AlaUGC, and at 25/26 of tRNA-GluUUC in the C. maquilingensis geno […]

library_books

tRNA gene diversity in the three domains of life

2014
Front Genet
PMCID: 4033280
PMID: 24904642
DOI: 10.3389/fgene.2014.00142

[…] ry leader sequence that forms the characteristic BHB motif at the tRNA exon-intron boundary. In an attempt to find structurally disrupted tRNA genes, our team developed a new tRNA prediction software SPLITS and SPLITSX (Sugahara et al., , ) that centers on finding multiple intron-containing tRNA and split tRNA through detection and removal of BHB motifs at the genome level. For similar reasons, im […]

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SPLITS institution(s)
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan

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