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Protocols

WebACT specifications

Information


Unique identifier OMICS_17871
Name WebACT
Interface Web user interface
Restrictions to use None
Input data A genome sequence.
Input format raw, EMBL or FASTA format
Programming languages Java
Computer skills Basic
Stability No
Maintained No

Publication for WebACT

WebACT citations

 (66)
library_books

Predominant gut Lactobacillus murinus strain mediates anti inflammaging effects in calorie restricted mice

2018
Microbiome
PMCID: 5863386
PMID: 29562943
DOI: 10.1186/s40168-018-0440-5

[…] rated to substitute DNA-DNA hybridization (DDH) to circumscribe species at genomic level.At the nucleotide level, pairwise genome alignment of the two strains of Lactobacillus spp. was generated with WebACT (BLASTN with default parameters) [] and visualized with the Artemis Comparison Tool (ACT, score cutoff with 2000) []. For the analysis, the replication origin of each genome was located with th […]

library_books

Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms

2018
Genome Biol Evol
PMCID: 5888409
PMID: 29617810
DOI: 10.1093/gbe/evy059

[…] and six NAP1/ST01 were selected for further analyses. To spot unshared regions resembling MGEs, contigs containing unique gene clusters were compared with cognate contigs from reference genomes using WebACT/ACT (). For MGE delimitation, we considered criteria such as presence of genes from known MGEs (i.e., phage-related proteins or recombinases), % GC skews, and atypical codon usages. Putative MG […]

call_split

From the wound to the bench: exoproteome interplay between wound colonizing Staphylococcus aureus strains and co existing bacteria

2018
PMCID: 5955179
PMID: 29233035
DOI: 10.1080/21505594.2017.1395129
call_split See protocol

[…] ference genome of S. aureus strain N315 (GenBank: NC_007795.1), B. thuringiensis serovar konkukian str. 97–27 (GenBank: NC_017200), and K. oxytoca strain E718 (GenBank: NC_018106) using blastN in the WebACT comparison tool (http://www.webact.org/WebACT/prebuilt#) and analyzed in detail by the Artemis Comparison Tool (ACT) software [, ]. Similarity matches were filtered based on their length (100 k […]

library_books

Exploring the Genomic Traits of Non toxigenic Vibrio parahaemolyticus Strains Isolated in Southern Chile

2018
Front Microbiol
PMCID: 5809470
PMID: 29472910
DOI: 10.3389/fmicb.2018.00161

[…] to 75% and 0 for lower coverage values. Finally, the distribution of each gene in every strain was recorded. For comparative analysis, nucleotide sequences were aligned by BLASTN and TBLASTX with the WebACT online resource () and visualized with the Artemis Comparison Tool (ACT) release 13.0.0 (). […]

call_split

Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae

2017
PLoS One
PMCID: 5728576
PMID: 29236737
DOI: 10.1371/journal.pone.0189163
call_split See protocol

[…] ording to the best hit coordinates and aligned with cps reference sequences of both best hit and expected serotype, for comparison. Alignments were done using the Artemis Comparison Tool (ACT) v6 and WebACT [].The impact of coverage and N50 on the serotyping quality between samples identified at the serotype level and samples identified as serogroup, subset or misidentified was evaluated with a Wi […]

call_split

Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T β MCA

2017
PLoS One
PMCID: 5598929
PMID: 28910295
DOI: 10.1371/journal.pone.0183564
call_split See protocol

[…] ng data was assembled de novo with DNASTAR’s SeqMan NGen (DNASTAR Inc.), and contigs were mapped against the reference L. johnsonii NCC533 genome with progressiveMauve [,]. Genomes were compared with WebACT and dotplots of translated open reading frames were generated with PROmer in Galaxy [–]. Sequence data is available under BioProject ID PRJNA315676. […]

Citations

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WebACT institution(s)
Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London, UK; Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Pathogen Sequencing Unit, Sanger Institute, Cambridge, UK
WebACT funding source(s)
This work was supported by the Faculties of Life Sciences and Medicine, Imperial College London and the Wellcome Trust.

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