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DAS specifications


Unique identifier OMICS_29331
Name DAS
Alternative name Dense Alignment Surface
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Dense Alignment Surface

DAS citations


Identification of boric acid as a novel chemoattractant and elucidation of its chemoreceptor in Ralstonia pseudosolanacearum Ps29

Sci Rep
PMCID: 5561266
PMID: 28819159
DOI: 10.1038/s41598-017-09176-3

[…] phobic membrane-spanning region, and a hydrophilic cytoplasmic domain. Chemotactic ligands are known to bind to the periplasmic domains (i.e., LBDs) of MCPs, thereby initiating chemotactic signaling. Dense alignment surface analysis identified the LBD of McpB as a region spanning 157 aa (residues 33 to 187). To determine whether McpB recognizes boric acid directly, the LBD of McpB was overexpresse […]


Disparate thermostability profiles and HN gene domains of field isolates of Newcastle disease virus from live bird markets and waterfowl in Uganda

Virol J
PMCID: 4915153
PMID: 27329265
DOI: 10.1186/s12985-016-0560-0

[…] vels. The B- cell epitope of HN gene was predicted in a computer algorithm using web server based on software www.bioinfo.tsinghua.edu.cn/epitope/EPMLR. The transmembrane domains were predicted using Dense Alignment Surface (DAS) transmembrane domain prediction server– http:www.sbc.su.se/-miklos/DAS/maindashtml []. […]


HrcU and HrpP are pathogenicity factors in the fire blight pathogen Erwinia amylovora required for the type III secretion of DspA/E

BMC Microbiol
PMCID: 4875606
PMID: 27206522
DOI: 10.1186/s12866-016-0702-y

[…] ic cleavage and conformational change required for protein function [, ]. This NPTH motif is conserved in all known YscU/FlhB proteins [, , ]. Bioinformatic analysis of HrcU from E. amylovora using a dense alignment surface algorithm predicted that, like YscU/FlhB homologs, HrcU encodes four transmembrane domains as well as a cytoplasmic C-terminal tail (Fig. ) [, ]. Using T-Coffee multiple alignm […]


A small mitochondrial protein present in myzozoans is essential for malaria transmission

Open Biol
PMCID: 4852462
PMID: 27053680
DOI: 10.1098/rsob.160034

[…] www.cbs.dtu.dk/services/SignalP/), TMHMM (http://www.cbs.dtu.dk/services/TMHMM-2.0/), TMPred (http://embnet.vital-it.ch/software/TMPRED_form.html), HHPred (http://toolkit.tuebingen.mpg.de/hhpred) and dense alignment surface DAS method []. The mitochondrial localization prediction algorithm MitoProt II (v. 1.101) was employed to assess possible export to this organelle []. Phylogenetic trees were c […]


Frequency and Fitness Consequences of Bacteriophage Φ6 Host Range Mutations

PLoS One
PMCID: 4237377
PMID: 25409341
DOI: 10.1371/journal.pone.0113078

[…] alignments and iterative structural assembly simulations. Default parameters were used for the I-TASSER submission. The P3 amino acid sequence was submitted to the transmembrane structure prediction Dense Alignment Surface software (DAS) website (http://www.sbc.su.se/~miklos/DAS/maindas.html). DAS uses low-stringency dot-plots of the query sequence against a collection of non-homologous membrane […]


Deorphanizing the human transmembrane genome: A landscape of uncharacterized membrane proteins

Acta Pharmacol Sin
PMCID: 3880479
PMID: 24241348
DOI: 10.1038/aps.2013.142

[…] divide a protein's hydrophobicity profile into transmembrane and cytosolic elements. Similarly, alignment methods extend this idea by seeking supporting information across multiple proteins, such as dense alignment surface (DAS) and transmembrane multiple alignment prediction (TMAP), which generate consensus dot plots comparing the hydropathy profile of the protein of interest to a collection of […]


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DAS institution(s)
Institute of Enzymology, Biological Research Center Hungarian Academy of Sciences, Budapest, Hungary; Department of Biochemistry, Stockholm University, Stockholm, Sweden
DAS funding source(s)
Supported by a cooperation framework of the Royal Swedish Academy of Sciences and the Hungarian Academy of Sciences, and by grants from the Swedish Technical Sciences Research Council (TFR), the Magnus Bergvall foundation and from the Swedish Natural Profile Research Council.

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