EzBioCloud

[…] e reference strains of actinobacteria from the NCBI genomic database using a BLASTn search to determine similarity percentages. The strains with highest similarity percentages were retrieved from the EzTaxon database [], and multiple sequence alignment was performed using Clustal W software packaged in MEGA 6.0 []. The evolutionary models were selected based on the lowest Bayesian information crit […]

[…] 3730XL DNA Analyzer from Life Sciences Solutions Group, Thermo Fisher Scientific (Beijing). The genus-level affiliation of the sequences was validated using available 16S rRNA gene sequences from the EzTaxon-e server (). Sequence alignment and phylogenetic analysis were carried out using MEGA version 5 (). Phylogenetic trees were constructed by using the neighbor-joining method () with bootstrap v […]

[…] ious step. The FastTree2 software implemented in this software was used to infer an approximated maximum-likelihood tree (; ). The 16S rRNA gene sequences of the same species were downloaded from the EzBioCloud database and aligned manually using secondary structure information by the EzEditor2 program () and a maximum-likelihood phylogenetic tree reconstructed using RAxML with the GTRGAMMA model […]

[…] orward and reverse 16S rRNA gene sequences, obtained from each strain, were assembled and analyzed using Basic Local Alignment Search Tool (). To identify the isolates, the sequences were uploaded to EzTaxon server () and compared with 16S rRNA gene sequence of the type strains. The Ribosomal Database Project online tool () was used to align the sequences with the related 16S rRNA gene sequences f […]

[…] olonies with a diameter of less than 1 mm on agar plates containing iron and manganese. BLAST searches of a 1,504-bp sequence of the 16S RNA gene using the Nucleotide Collection Nr/Nt database () and EzBioCloud () revealed five of the seven described Kineosporia strains as the closest relatives, namely, strains NBRC 16234T, JCM 9954T, VN05A0415T, JCM 9957T, and YIM 65293T, each with an identity of […]

[…] ins, namely, Novosphingobium hassiacum strain W-51 (98%) and Novosphingobium aromaticivorans DSM 12444 (98%), based on BLASTn searches (), and 97.6% similarity to Novosphingobium ginsenosidimutans by EzBioCloud () searches.The Gram-negative rod-shaped Novosphingobium strain B 225 was isolated from a 4-month-old iron- and manganese-depositing biofilm grown in a continuous-flow biofilm reactor expos […]