tRNAscan-SE

[…] study, Klimov & OConnor provided an improved tRNA prediction in the house dust mite Dermatophagoides farinae including tRNAs of S. magnus for a comparison. Like Domes et al., Klimov and OConnor used tRNAscan-SE and ARWEN to predict tRNAs and infer their secondary structure. In contrast to Domes et al., the minimum free energy (MFE) of the constrained and unconstrained secondary structure was addi […]

[…] s, in genes with HSPs, and in HSP regions (Supplementary Figs. , ) were calculated from the results of BLAST searches against the BUSCO Ascomycota ‘ancestral’ database.tRNA genes were predicted using tRNAscan-SE, with introns removed by our own Python code. In some Kluyveromyces species, the tLCAG gene was not predicted by tRNAscan-SE due to its unusually long intron but was found by BLASTN. In ou […]

[…] d open-reading frames (ORF) were analyzed using program MEGA 5.0 []. The overlapping regions and intergenic spacers were counted manually []. The tRNA genes were identified using the software package tRNAscan-SE 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/) by eye, based on vertebrate mitochondrial anti-codon sequences and their secondary structure. In addition, the DOGMA annotation software was used […]

[…] A and ORF finder (NCBI), and were confirmed by comparing nucleotide sequences with those from closely related nematodes. Putative secondary structures of 22 tRNA genes were inferred using the program tRNAscan-SE and verified by examining potential tRNA secondary structures and anticodon sequences. […]

[…] stop codons and intron–exon boundaries were manually annotated based on previously annotated information from the close relative A. thaliana. The complete structure of tRNA genes was validated using tRNAscan-SE v1.2.1. The systematic circular view of the chloroplast genome was created using OGDRAW and in-house customized perl script. Comparative syntenic maps were generated using circos following […]

[…] tion annotation was performed using the BLAST tools at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) against the non-redundant protein sequences database. Transfer RNAs (tRNAs) were identified using tRNAscan-SE (v1.23, http://lowelab.ucsc.edu/tRNAscan-SE) and ribosome RNAs (rRNAs) were determined using RNAmmer (v1.2, http://www.cbs.dtu.dk/services/RNAmmer/). DNAman was used to calculate molecular […]