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CDvist specifications

Information


Unique identifier OMICS_07066
Name CDvist
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for CDvist

CDvist citations

 (6)
library_books

A widespread family of polymorphic toxins encoded by temperate phages

2017
BMC Biol
PMCID: 5576092
PMID: 28851366
DOI: 10.1186/s12915-017-0415-1

[…] ns and clustered them with Single Linkage Clustering of Sequences (SiLiX, sequence identity ≥ 30% and overlap ≥ 50%) []. We obtained eight families with more than five sequences. Domain analysis with CDvist tool [] showed that four of these families have hits within the C-terminal region of COG2369, which is a cluster of orthologous groups including proteins with a MuF1 domain. The profile Ct_MAD […]

library_books

Fungal Hybrid B heme peroxidases – unique fusions of a heme peroxidase domain with a carbohydrate binding domain

2017
Sci Rep
PMCID: 5571214
PMID: 28839281
DOI: 10.1038/s41598-017-09581-8

[…] o CBM21 and CBM34 families. We have selected CfioHyBpox1, CgloHyBpox3 and MagHyBpox1 that revealed in the first round of screening the highest probability for the presence of CBM domains by using the CDvist suite. It has to be emphasized that both CBM21 and CBM34 belong to the so-called raw starch-binding domains (SBD) found typically as modules of various microbial amylolytic enzymes. Among 81 cu […]

library_books

Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome

2017
Front Plant Sci
PMCID: 5470089
PMID: 28659964
DOI: 10.3389/fpls.2017.01037

[…] ene Structure Display Server v2.0 () by aligning the cDNA sequences with the corresponding genomic DNA sequences. The functional motifs or domains of putative TF protein sequences were analyzed using CDvist (). For phylogenetic analysis, multiple sequence alignments of the full-length protein sequences were performed using MUSCLE v3.8.31 with maxiters set at 1000. The acquired alignment was used t […]

library_books

The activity of a yeast Family 16 methyltransferase, Efm2, is affected by a conserved tryptophan and its N‐terminal region

2016
FEBS Open Bio
PMCID: 5324768
PMID: 28255539
DOI: 10.1002/2211-5463.12153

[…] ly 16 methyltransferases were aligned using Clustal Omega . This alignment was then used to generate a sequence logo using Web logo . The domain structures of Family 16 proteins were visualised using CDvist . Efm2 was modelled with Swiss‐Model based on the structure of METTL21D (PDB ID: 4LG1) and disorder predicted by pondr‐fit . Structures of METTL21A‐D were acquired from the RCSB Protein Data B […]

library_books

Proceedings of the 15th Annual UT KBRIN Bioinformatics Summit 2016

2016
BMC Bioinformatics
PMCID: 5001208
PMID: 28166713
DOI: 10.1186/s12859-016-1154-y

[…] O, Reznik AO, Ory DS, Zhulin IB: Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations. Genet Med 2016.26. Adebali O, Ortega DR, Zhulin IB: CDvist: a webserver for identification and visualization of conserved domains in protein sequences. Bioinformatics 2015, 31(9):1475-1477.27. Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Micha […]

library_books

Establishing the precise evolutionary history of a gene improves prediction of disease causing missense mutations

2016
Genet Med
PMCID: 4990510
PMID: 26890452
DOI: 10.1038/gim.2015.208

[…] To build domain architectures, we used the CDvist Web server with HMMER3 against Pfam 27.0 and HHsearch against Protein Data Bank options., Protein Data Bank HHsearch probability cutoff was adjusted to 98%.We implemented the SAVER algorithm in […]

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CDvist institution(s)
Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA

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