Sentence examples for bacterial sequences obtained from from inspiring English sources
Sequences were also analyzed by BLAST [44] searches in GenBank database (http://www.ncbi.nlm.nih.gov) and were aligned with representative bacterial sequences obtained from the public databases using ClustalX software [45].
All effective bacterial sequences obtained from pyrosequencing in this study were compared with Greengenes 16S rRNA gene database (DeSantis et al. 2006) annotated with NCBI taxonomy using NCBI's BLASTN tool (Altschul et al. 1990) and the default parameters except for the maximum hit number of 100 (Claesson et al. 2009).
For each bacterial species, sequences obtained from this study and predicted to fold with a free energy lower than -5 Kcal/mol were selected.
This database was originally set up as a repository for bacterial type sequences obtained from the databases RDP, SILVA and Greengenes.
For application of the classifiers to protein sequences (obtained from bacterial genome data), an average score was computed from the individual window scores.
All 11 sequenced plasmid inserts from these xylanase-positive yeast colonies encoded GH11 proteins (ranged between 221 and 289 amino acids in length); 5 of them had already been identified among sequences obtained from bacterial colonies and 4 had a C-terminal CBM1 domain.
Within the main lineage, the sequences obtained from the bacterial strains associated with 31SR were formed in the branch separated from the sequences of other bacteria that were isolated from soil.
The partial 16S rRNA gene sequences obtained from the bacterial isolates have been deposited in the GenBank and ENA (European Nucleotide Archive) databases and the related accession number is reported in Table 6.
The partial 16S rRNA gene sequences obtained from the bacterial isolates and the excised DGGE bands have been deposited in the EMBL, respectively, under accession numbers HF678717 HF678862 and HF678127 HF678194.
This was confirmed by Huber et al. [ 15] who analyzed nearly 700,000 bacterial and ca. 200,000 archaeal V6 tag sequences obtained from two biogeochemically distinct hydrothermal vents.
We analyzed the robustness of two statistics most commonly used in MLST studies -the percentage of variable sites and the nucleotide diversity (π, [43])- using concatenated DNA sequences obtained from MLST data of several bacterial species (Table 1).
