We report the 5.7-Mb draft genome sequence of Aneurinibacillus tyrosinisolvens strain LL-002(T), isolated from organic- and methane-rich sea sediments. The draft genome sequence of strain LL-002(T) consists of 5,693,818 bp in 136 contigs, with a G+C content of 44.5%, 5,946 potential coding sequences (CDS), 2 rRNAs, and 39 tRNAs.

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Conserved non-coding elements (CNEs) are defined using various degrees of sequence identity and thresholds of minimal length. Their conservation frequently exceeds the one observed for protein-coding sequences. We explored the chromosomal distribution of different classes of CNEs in the human genome. We employed two methodologies: the scaling of block entropy and box-counting, with the aim to a...

for each media condition as the extent of survival and reproduction (fitness) of the deletion strain relative to the pool of all strains grown and measured collectively. Fitness values (f) of 1.0 indicate no difference between a single strain and the pool average for that condition; f , 1.0 indicates that the strain is less fit, and f . 1.0 indicates that the strain is more fit than the pool av...

The codon preference plot is useful for locating genes in sequenced DNA, predicting the relative level of their expression and for detecting DNA sequencing errors resulting in the insertion or deletion of bases within a coding sequence. The three possible reading frames are displayed in parallel along with the open reading frames and plots of the location of rare codons in each reading frame.

Escherichia coli endonuclease VIII and endo-nuclease III are oxidative base excision repair DNA glycosylases that remove oxidized pyrimidines from DNA. The genes encoding these proteins, nei and nth, are both co-transcribed as the terminal genes in operons. nei is the terminal gene in an operon with four open reading frames that encode proteins of unknown function. This operon has two confirmed...

Genomic DNA sequence was determined for the putative Neurospora crassa ABC transporter NCU09975 from several different classical mutant strains including several acriflavin resistant mutants. The sensitivity of these strains to acriflavin was tested. While the open reading frame NCU09975 has multiple polymorphisms in strains sequenced for other purposes, none of the acriflavin resistant classic...

In fish vaccinology, the secondary antibodies against fish immunoglobulins (Igs) are necessary to measure specific humoral immune responses in immunized fish. In the present study, polyclonal antiserum against olive flounder (Paralichthys olivaceus) IgM heavy chain was generated by intramuscular immunization of rabbit with Escherichia coli/eukaryotic shuttle vector containing open reading frame...

Identifying genes encoding bacteriocins and ribosomally synthesized and posttranslationally modified peptides (RiPPs) can be a challenging task. Especially those peptides that do not have strong homology to previously identified peptides can easily be overlooked. Extensive use of BAGEL2 and user feedback has led us to develop BAGEL3. BAGEL3 features genome mining of prokaryotes, which is largel...

When using EZ-TN5 Transposomes to create gene knockouts or to insert open reading frames, control elements, regulatory elements and antibiotic resistances into bacteria, there are number of considerations that must be made in order to plan for a successful transposition event in vivo. The three main considerations given below should be examined prior to performing in vivo transposition reaction...