tRNAscan-SE

[…] prodigal version 1.20 (), genemarks version 4.08 (), and protein blast () and confirmed by the rapid annotations using subsystems technology (rast) version 2.0 server (). trnas were predicted using trnascan-se version 2.0 (), and the nucleotide homology of pvco-5 was determined using emboss stretcher ()., the genome of pvco-5 comprised double-stranded linear dna of 74,325 bp and a g+c content […]

[…] construction with pacbio rs ii and illumina hiseq dna to determine the complete genomic sequence of the b. melitensis qh61. the annotation was performed using genemarks (), repeat masker (), trf (), trnascan-se (), and rnammer ()., the whole-genome sequence of b. melitensis qh61 was found to be 3,311,767 bp in size and to be composed of two circular chromosomes, chromosome i (2,126,173 bp) […]

[…] assembled with a5-miseq software (). genome and subsystem-based annotations were performed by rapid annotation using subsystem technology (rast) (, ). trna gene detection was performed using the trnascan-se 2.0 tool (), whereas rrna genes were predicted using rnammer (). plasmid presence was checked by plasmidfinder software ()., after assembly, the two genomes were composed of 99 scaffolds. […]

[…] the previously known plasmid, pkap, of 41.7 kb (). the genome contains three rrna clusters in 16s-23s-5s configurations., gene annotation of the draft sequence was carried out using prodigal (), trnascan-se (), and rnammer () software tools. next to 36 trna genes, 1,080 protein coding sequences could be identified, of which, 787 could be functionally annotated by a similarity search […]

[…] (altschul et al., ) and brig (alikhan et al., ). the presence of phages was screened using phaster (http://phaster.ca/) (arndt et al., ). trnas were screened using trna-se (http://lowelab.ucsc.edu/trnascan-se/) (lowe and chan, )., draft whole-genome sequence of strain sckp83 has been deposited into genbank under the accession number nokm00000000. short reads of the whole-genome sequence […]

[…] 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 […]

[…] 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., the datasets generated during and/or analysed during the current study are available […]

[…] 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 […]

[…] 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 […]

[…] with the protein function if it located in the same cluster as the annotated query sequence. gene ontologies (go) were annotated by blast2go software []. trna genes were identified with softwares trnascan-se [] and aragorn []., we defined genes with biased expression as either those homoeologous genes, with higher rpkm values two-fold or greater than the paired gene, as in previous studies […]