DNA Baser Sequence Assembler protocols

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DNA Baser Sequence Assembler specifications

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Unique identifier OMICS_02139
Name DNA Baser Sequence Assembler
Software type Package/Module
Interface Graphical user interface
Restrictions to use License purchase required
Biological technology Roche
Operating system Unix/Linux, Windows
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes

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  • person_outline D Baser Sequence Assembler Team <>

DNA Baser Sequence Assembler in pipelines

 (6)
2017
PMCID: 5615607
PMID: 28914802
DOI: 10.3390/ijerph14091070

[…] if primer 8f failed, only partial sequencing was obtained. a contiguous sequence was constructed with forward and reverse sequencing data resulting in a fragment of approximately 1400 bp, with dna baser sequence assembler v4 (2013) (heracle biosoft, arges, romania)., sequences were compared with those in the ncbi database (genbank) using the blast sequence analysis tool [], and eztaxon-e […]

2016
PMCID: 4711807
PMID: 26741495
DOI: 10.1371/journal.pone.0146558

[…] 16s rrna gene clone library were analyzed systematically. nucleotide sequences were manually checked, forward and reverse complementary sequences were assembled and trimmed of vector sequences using dna baser sequence assembler software (heracle biosoft s.r.l., pitesti, romania). chimera sequences were detected and further removed by the web-based version of the usearch 6.0 chimera detection […]

2016
PMCID: 4814864
PMID: 26822469
DOI: 10.1111/irv.12373

[…] strains described in this study were submitted to genbank under the accession numbers: kr059989–kr060014., consensus contig assembly of the newly determined nucleotide sequences was performed using dna baser sequence assembler v.4 (2013) (heracle biosoft, www.dnabaser.com) and thereafter edited using bioedit sequence alignment editor. multiple sequence alignment was performed using muscle […]

2015
PMCID: 4364345
PMID: 25727040
DOI: 10.3325/cmj.2015.56.32

[…] of abi prism 3130xl genetic analyzer (applied biosystems) (gel pop 7, capillary 36 cm). the obtained sequences were aligned using clustal w, v. 2.0.12 () contained in bioedit, v. 7.0.8.0 (), and dna baser sequence assembler, v. 4.10.1.13 ()., for the purpose of species identification, the obtained sequences were compared with sequences available in the national center for biotechnology […]

2015
PMCID: 4520198
PMID: 26223795
DOI: 10.1186/s12879-015-1060-3

[…] reaction kit; applied biosystems). about 1.25 μl of primers hbpr2 and hbpr3 were used for forward and reverse sequencing reactions, respectively. pairwise contiguous sequences were generated using dna baser sequence assembler version 4.20.0 (heracle software, germany). consensus sequences were aligned with complete hbv genotypes a-j reference sequences from genbank using clustalw []. […]


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DNA Baser Sequence Assembler in publications

 (23)
PMCID: 5784674
PMID: 29416558
DOI: 10.1186/s13068-018-1012-4

[…] for 7 min. pcr products were purified and sequenced at gatc (konstanz, germany). the 16s rrna gene sequences of the isolates were checked for reading errors, trimmed and aligned using the programme dna baser sequence assembler v4 (heracle biosoft s.r.l, arges, romania), and then the partial sequences of 16s rrna genes were blasted against the ncbi online database., principal coordinate analysis […]

PMCID: 5557520
PMID: 28806900
DOI: 10.1186/s12862-017-1022-z

[…] 2011), each of the eight amplicon pools were analyzed independently. in total, eight fastq files were generated and transformed into fasta (multifasta) files using avalanche nextgen package (dna baser sequence assembler v4 (2013), heracle biosoft, www.dnabaser.com). the jmhc software [] was used to remove primer sequences and unique tags, and to generate alignments of all variants per […]

PMCID: 5297017
PMID: 28173748
DOI: 10.1186/s12862-017-0897-z

[…] sequenced on both strands with a big dye terminator sequencing kit (v3.1 thermo fisher scientific), and run on an applied biosystems abi 3130 xl genetic analyzer. sequences were assembled using dna baser sequence assembler version 4.10. a summary of all variants identified through resequencing is available (fig. , table , additional file : table s6 and s7)., genetic association […]

PMCID: 5408719
PMID: 28462032
DOI: 10.7717/peerj.3223

[…] protocol. purified amplicons were sent for sanger sequencing to macrogenusa (cambridge, ma) using the amplification primers. a consensus contiguous sequence for each isolate was constructed using dna baser sequence assembler v3.5.4 software (heracle biosoft s.l.r. pitest, romania). putative fungal identities were then determined using the blast algorithm () and the genbank database., […]

PMCID: 5167363
PMID: 27992477
DOI: 10.1371/journal.pone.0168331

[…] the b. pseudomallei mlst website (www.http://bpseudomallei.mlst.net/) using the clustalw2-multiple sequence alignment-embl-ebi (www.ebi.ac.uk/tools/msa/clustalw2). dna sequences were edited using dna baser sequence assembler v4 (heracle biosoft, www.dnabaser.com). sequences obtained for each of the seven loci of individual bacterial isolates were given an allelic number using the online […]


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