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Protocols

SeqAssem specifications

Information


Unique identifier OMICS_05330
Name SeqAssem
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Input data Some DNA sequences.
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability Stable
Free trial Yes
Maintained Yes

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  • person_outline SeqAssem

SeqAssem citations

 (9)
library_books

Elizabethkingia miricola as an opportunistic oral pathogen associated with superinfectious complications in humoral immunodeficiency: a case report

2017
BMC Infect Dis
PMCID: 5727958
PMID: 29233117
DOI: 10.1186/s12879-017-2886-7

[…] ng the universal primers, 16S_Start 27F (5’-AGAGTTTGATCMTGGCTCAG-3′) and 16S_Stop 519R (5’-GWATTACCGCGGCKGCTG-3′). The products were sequenced by Sanger’s method, and the sequences were aligned using SeqAssem ver.07/2008. Homology with known sequences was searched using the EzTaxon database (http://www.ezbiocloud.net). The 522 bp sequence of the clinical isolate showed the highest homology (99.37% […]

call_split

Terrestrial adaptation of green algae Klebsormidium and Zygnema (Charophyta) involves diversity in photosynthetic traits but not in CO2 acquisition

2017
PMCID: 5633629
PMID: 28721563
DOI: 10.1007/s00425-017-2741-5
call_split See protocol

[…] Rindi ). Each 20 μL reaction solution for PCR was conducted as described by Ryšánek et al. (). The PCR protocol followed that of Škaloud and Rindi (). Sequencing reads were assembled and edited using SeqAssem software (Hepperle ). Newly obtained Klebsormidium rbcL sequence and the sequences available in the GenBank database were used to produce an alignment for phylogenetic analyses. The final ali […]

library_books

Variability in the sxt Gene Clusters of PSP Toxin Producing Aphanizomenon gracile Strains from Norway, Spain, Germany and North America

2016
PLoS One
PMCID: 5132012
PMID: 27907126
DOI: 10.1371/journal.pone.0167552

[…] A sequence of the 16S rRNA locus in A. gracile strain NIVA-CYA 851 and sequences of the sxt gene cluster in all four Aphanizomenon strains were analyzed using the Seqassem software package (version 07/2008) []. The Align MS Windows-based manual sequence alignment editor (version 03/2007) [] was used to obtain DNA sequence alignments, which were then corrected m […]

library_books

Phytoplankton Diversity and Community Composition along the Estuarine Gradient of a Temperate Macrotidal Ecosystem: Combined Morphological and Molecular Approaches

2014
PLoS One
PMCID: 3981767
PMID: 24718653
DOI: 10.1371/journal.pone.0094110

[…] All the sequences were manually checked, trimmed and edited using the SeqAssem software , and then compared to those available in public databases (GenBank) using the NCBI BLASTn web application . Potential chimeras were detected with the online softwares Bellerophon a […]

call_split

Molecular Phylogeny of the Leafy Liverwort Lejeunea (Porellales): Evidence for a Neotropical Origin, Uneven Distribution of Sexual Systems and Insufficient Taxonomy

2013
PLoS One
PMCID: 3867362
PMID: 24367522
DOI: 10.1371/journal.pone.0082547
call_split See protocol

[…] ne using BigDye® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA). Sequencing primers were those used for PCR. Newly generated sequences were assembled and edited using SeqAssem . Seven hundred and nineteen sequences were newly generated for this study; 175 sequences were downloaded from Genbank. […]

library_books

Congruence of chloroplast and nuclear encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae)

2013
BMC Evol Biol
PMCID: 3598724
PMID: 23402662
DOI: 10.1186/1471-2148-13-39

[…] ycle Sequencing v3.1 kit (Applied Biosystems, Darmstadt, Germany) and separated on an ABI Prism 3100 (Applied Biosystems, Darmstadt, Germany) sequencer. The sequences were assembled using the program SeqAssem []. For GenBank accession numbers of newly determined sequences for the 29 Heterococcus strains see Additional file ; the accession numbers for the four green algal sequences determined in th […]


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