Publications

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Sampling of Publications Citing DNAMAN Sequence Analysis Software

Role of Adenine Nucleotide Translocator 1 in mtDNA Maintenance
Jyrki Kaukonen, Jukka K. Juselius, Valeria Tiranti, Aija Kyttala, Massimo Zeviani, Giacomo P. Comi, Sirkka Keranen, Leena Peltonen, and Anu Suomalainen
Science 4 August 2000: 782-785.
...default parameters was used for multiple sequence alignment, and DNAMAN software (Lynnon Biosoft...default parameters was used for multiple sequence alignment, and DNAMAN software (Lynnon Biosoft) for graphical enhancement

Tetrapyrrole biosynthetic enzyme protoporphyrinogen IX oxidase 1 is required for plastid RNA editing
Fan Zhang, Weijiang Tang, Boris Hedtke, Linlin Zhong, Lin Liu, Lianwei Peng, Congming Lu, Bernhard Grimm, and Rongcheng Lin
PNAS, Feb 2014; 111: 2023 - 2028.
... ...1316183111 7 of 11 Fig. S9. Protein alignment of PPO1 and PPO2 from various species. The alignment was generated using DNAMAN with default parameters. The positions of conserved residues are shown in black, and similar residues are shown in turquoise...

Trypanosoma brucei Vacuolar Transporter Chaperone 4 (TbVtc4) Is an Acidocalcisome Polyphosphate Kinase Required for in Vivo Infection
Noelia Lander, Paul N. Ulrich, and Roberto Docampo
J. Biol. Chem., Nov 2013; 288: 34205 - 34216.
... ...analytical grade were from Sigma. Sequence Analysis The analysis of TbVtc4 sequence (gene ID Tb11.01.4040) was performed using DNAMAN software (version 7.212, Lynnon Corp., Quebec, Canada) for alignments, BLAST for searching homologous sequences, the... ...

Extensive Gene Acquisition in the Extremely Psychrophilic Bacterial Species Psychroflexus torquis and the Link to Sea-Ice Ecosystem Specialism
Shi Feng, Shane M. Powell, Richard Wilson, and John P. Bowman
Genome Biol Evol, Jan 2014; 6: 133 - 148.
... ...important evidence for HGT in regions of a genome (Ochman et al. 2000). Thus, we plotted the overall GC% of P. torquis using DNAMAN. The overall GC% of P. torquis is 34.5%, and we were able to locate several regions that deviated from this mean ranging... ...

TET2 Plays an Essential Role in Erythropoiesis by Regulating Lineage-Specific Genes via DNA Oxidative Demethylation in a Zebrafish Model
Liang Ge, Rui-peng Zhang, Feng Wan, Dong-yang Guo, Ping Wang, Li-xin Xiang, and Jian-zhong Shao
Mol. Cell. Biol., Mar 2014; 34: 989 - 1002.
... ...the UCSC Genome Bioinformatics website ( http://genome.ucsc.edu/ ), and the methylation status was analyzed by using DNAMan (Lynnon Corporation, Canada). Statistical analysis. All experiments were replicated at least three times. All data are... ...

Unusual characteristics of dicistrovirus-derived small RNAs in the small brown planthopper, Laodelphax striatellus
Junmin Li, Ida Bagus Andika, Yanru Zhou, Jiangfeng Shen, Zongtao Sun, Xu Wang, Liying Sun, and Jianping Chen
J. Gen. Virol., Mar 2014; 95: 712 - 718.
...and could therefore be assembled into a full genome using dnaman 6 (Fig. 1a). The sequences of the RT-PCR products amplified...98-98.5% in the capsid protein precursor (analysed using dnaman 6). To determine the abundance of HiPV sRNAs in each of the...

Wickerhamomyces arborarius f.a., sp. nov., an ascomycetous yeast species found in arboreal habitats on three different continents
Stephen A. James, Enrique Javier Carvajal Barriga, Patricia Portero Barahona, Thomas C. Harrington, Ching-Fu Lee, Christopher J. Bond, and Ian N. Roberts
Int J Syst Evol Microbiol, Mar 2014; 64: 1057 - 1061.
... ...related taxa, retrieved from EMBL, using the multiple alignment program clustal w (Thompson et al., 1994), included in the dnaman software package, version 5.1.5 (Lynnon BioSoft). A phylogenetic tree was reconstructed using the neighbour-joining...

A Novel Group of Glutaredoxins in the cis-Golgi Critical for Oxidative Stress Resistance
Nikola Mesecke, Anne Spang, Marcel Deponte, and Johannes M. Herrmann
Mol. Biol. Cell, Jun 2008; 19: 2673 - 2680.
... ...Bootstrap numbers are indicated. The tree was calculated using the DNAman software package (Lynnon, Quebec, Canada). Grx6 and Grx7...Hydrophobicity profiles of Grx6 and Grx7 were generated using the DNAman software. N-terminal hydrophobic regions of the proteins...

Evolution of small nucleolar RNAs in nematodes
Anja Zemann, Anja op de Bekke, Martin Kiefmann, J�rgen Brosius, and J�rgen Schmitz
Nucleic Acids Res.,�May 2006; 34: 2676 - 2685.
... ...search strategies based on a modified�DNAMAN�program, we characterized 151 npcRNAs...strategies The commercial software package�DNAMAN�was modified, in collaboration with the...compiled RNA databases. The modified�DNAMAN�version is available from http://www.lynnon.com

Expression Profiling of the 14-3-3 Gene Family in Response to Salt Stress and Potassium and Iron Deficiencies in Young Tomato (Solanum lycopersicum) Roots: Analysis by Real-time RT�PCR
WEI FENG XU and WEI MING SHI
Ann. Bot.,�Nov 2006; 98: 965 - 974.
... ...phylogenetic tree creation were performed using�DNAMAN�version 4.0 (Lynnon Biosoft Company...phylogenetic trees were performed using�DNAMAN�version 4.0 (Lynnon Biosoft Company...1. The dendrogram was produced using�DNAMAN�version 4.0 (Lynnon Biosoft... ...

A New Arg54Gly Transthyretin Gene Mutation Associated With Vitreous Amyloidosis In Chinese
Yining Shi
Invest. Ophthalmol. Vis. Sci.,�Apr 2011; 52: 64.
... ...were amplified by polymerase chain reaction(PCR). The gene fragments were sequencing, and the results were analyzed with�DNAMAN�Windows 5.2.2.0 and the Chromas sequence chart analysis software and the normal human TTR gene exons were compared with... ...

Streptomyces polyantibioticus�sp. nov., isolated from the banks of a river
Marilize le Roes-Hill and Paul R. Meyers
Int J Syst Evol Microbiol,�Jun 2009; 59: 1302 - 1309.
... ...cavourensis NBRC 13026T by pairwise local alignment in�dnaman, version 4.13; Lynnon BioSoft, Streptomyces caviscabies ATCC 51928T in�dnaman�and Streptomyces setonii ATCC 25497T in�dnaman�and various other members of the genus Streptomyces... ...

Kribbella�albertanoniae�sp. nov., isolated from a Roman catacomb, and emended description of the genus�Kribbella
Gareth J. Everest, Sarah M. Curtis, Filomena De Leo, Clara Urz�, and Paul R. Meyers
Int J Syst Evol Microbiol,�Oct 2013; 63: 3591 - 3596.
... ...Sequence analysis was performed using�dnaman�version 5.2.9 (Lynnon BioSoft...similarity over 1455 bp, by local alignment in�dnaman) and Kribbella yunnanensis YIM 30006T (99.11%, 1464 bp,�dnaman). This association was confirmed by... ...

C-terminal processing of reaction center protein D1 is essential for the function and assembly of photosystem II in Arabidopsis
Yufen Che, Aigen Fu, Xin Hou, Kent McDonald, Bob B. Buchanan, Weidong Huang, and Sheng Luan
PNAS, Oct 2013; 110: 16247 - 16252.
... ...At5g46390, and Synechocystis PCC 6803 CtpA. The percentage indicates the similarity among different amino acid sequences. DNAMAN program was used in this analysis. Che et al. www.pnas.org/cgi/content/short/1313894110 1 of 3 Fig. S2. Flanking... ...

Salicylic acid 3-hydroxylase regulates Arabidopsis leaf longevity by mediating salicylic acid catabolism
Kewei Zhang, Rayko Halitschke, Changxi Yin, Chang-Jun Liu, and Su-Sheng Gan
PNAS, Sep 2013; 110: 14807 - 14812.
... ...its homologs and the phylogenetic tree was generated by with DNAMAN software (version 7). Zhang et al. www.pnas.org/cgi...3-hydroxylase enzyme (F3H). The alignment was done with DNAMAN software (version 7). 0 5 10 15 20 25 30 35 40 45 4 10 15... ...

Rapid hierarchical assembly of medium-size DNA cassettes
Jonathan Leo Schmid-Burgk, Zhen Xie, Stefan Frank, Sebastian Virreira Winter, Sibylle Mitschka, Waldemar Kolanus, Andrew Murray, and Yaakov Benenson
Nucleic Acids Res., Jul 2012; 40: e92.
... ...A bases. In addition, the lack of secondary structure was confirmed by simulation with DNAman software ( http://en.bio-soft.net/format/DNAMAN.html ). The resulting IDs are given in Table 1. The prospective junctions between the... ...

Analysis of the Microbial Community Structure by Monitoring an Hg Methylation Gene (hgcA) in Paddy Soils along an Hg Gradient
Yu-Rong Liu, Ri-Qing Yu, Yuan-Ming Zheng, and Ji-Zheng He
Appl. Envir. Microbiol.,�May 2014; 80: 2874 - 2879.
... ...microbes retrieved from the NCBI database (see Table S2 in the supplemental material). Selected hgcA sequences were aligned with�DNAMAN�(version 7.0; Lynnon Biosoft, USA) and are shown in Fig. S1. Forward (hgcA4F; 5-GGNRTYAAYRTCTGGTGYGC-3) and reverse... ...

C-reactive protein: a predominant LPS-binding acute phase protein responsive to Pseudomonas infection
Patricia M.L. Ng, Zhenxiao Jin, Sandra S.H. Tan, Bow Ho, and Jeak L. Ding
Journal of Endotoxin Research,�Jun 2004; 10: 163 - 174.
... ...references. Alignment was per- formed on�DNAman�v. 4.15 (Lynnon BioSoft). Optimal...3-UTR of CRP gene was constructed by�DNAman�v. 4.15, based on the sequence alignment...penalty and gap extension penalty on the�DNAman�software was set at 5 for generation of... ...

Molecular cloning, expression, and anti-tumor activity of a novel serine protease from�Arenicola cristata
Chunling Zhao and Jiyu Ju
Acta Biochim Biophys Sin,�Apr 2014; 10.1093/abbs/gmu020.
... ...accession number KF830712. Sequence analysis�DNAMAN�version 5.2.2 software was used for...amino acid sequences was done with the�DNAMAN�software. Phylogenetic analysis The phylogenetic...of the other proteases from annelid.�DNAMAN�1, 2, 3, 4 stands for E. fetida... ...

Bacillus tequilensis�sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to�Bacillus subtilis
Joshua W. Gatson, Bruce F. Benz, Chitra Chandrasekaran, Masataka Satomi, Kasthuri Venkateswaran, and Mark E. Hart
Int J Syst Evol Microbiol,�Jul 2006; 56: 1475 - 1484.
... ...and sequence similarity was assessed using�DNAMan�software Lynnon BioSoft. Likewise,�DNAMan�software was used to align and determine the...also aligned and similarity was assessed using�DNAMan�software. Phylogenetic relationships between... ...

First report of tomato spotted wilt virus in Iberis semperflorens
G Parrella, L Cavicchi,�B Greco, MG Bellardi
Journal of Plant Pathology, 2013 Vol.95, S4.73
...�HG475336) which was compared with other TSWV sequences available in Gen- Bank using DNAMAN. The partial CP sequence showed 99.5% nucleotide identity with several Italian TSWV isolates (HQ839729-31, DQ376177-9, DQ376183, DQ915946).�...

Conservation and function of Dazl in promoting the meiosis of goat male germline stem cells
Z Niu, Y Hu, M Liao, M Yu, H Zhu, L Wang, J Wu
Molecular biology Reports, Jan 2014
...�The sequences in this test were all from NCBI (The websites in this study are all listed in Table 2). The sequences were aligned and the phylogenetic tree was depicted with�DNAMAN�software.�... Hydrophobicity of DAZL protein of mouse and goat were predicted by�DNAMAN.�...

Molecular Cloning, Sequence Analysis of Thioesterases from Wintersweet (Chimonanthus Praecox)
LH Zhang, Q Wu, XF Zou, LN Chen, SY Yu
Frontier and Future Development of Information Technology in Medicine and Education Lecture Notes in Electrical Engineering Volume 269, 2014, pp 2615-2621
...�The Hydrophobicity profile predicted of FAT amino acid sequence by�DNAMAN�and MEGA4x1 software.�...�327.5). Fig. 327.5 Secondary structure prediction of CpFATB. The software of�DNAman are applied to analyze to these FATs in clustering (Fig. 327.6).�...

MOLECULAR CHARACTERIZATION OF THE 16SR II GROUP OF PHYTOPLASMA ASSOCIATED WITH FABA BEAN (Vicia faba L.) IN SAUDI ARABIA
MA Al-Saleh, MA Amer
Journal of Animal and Plant Sciences, Jan 2014, 24:221-228
...�Analyses of the obtained sequences were carried out using the�DNAMAN�software trial version 5.2.10 program (Lynnon BioSoft, Canada).�...�The similarity analysis was calculated using the DNAMAN�Alignment software analysis. Accession No. Phytoplasma Name�...

Molecular cloning, expression and oxidative stress response of a mitochondrial thioredoxin peroxidase gene (AccTpx-3) from Apis cerana cerana
P Yao, W Lu, F Meng, X Wang, B Xu, X Guo
Journal of insect physiology, March 2013, 59: 273-282
...�NCBI bioinformatics tools (http://blast.ncbi.nlm.nih.gov/Blast.cgi) were used to detect conserved domains in AccTpx-3.�DNAman�version 5.2.2 (Lynnon Biosoft, Quebec, Canada) was used to search for the ORF of AccTpx-3. The tertiary structure was predicted using SWISS�...