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BASys specifications

Information


Unique identifier OMICS_04225
Name BASys
Alternative name Bacterial Annotation System
Interface Web user interface
Restrictions to use None
Input data DNA sequence data, an optional list of gene identification information
Input format Raw
Output data It provides extensive textual and hyperlinked image output.
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Bacterial Annotation System

BASys citations

 (77)
library_books

Efficient Visible Light Communication Transmitters Based on Switching Mode dc dc Converters

2018
PMCID: 5948605
PMID: 29642455
DOI: 10.3390/s18041127

[…] ing power supply is implemented using an isolated dc-dc converter ISF1209 A from XP Power (Singapore). Finally, The PWM signals used to drive the converter are calculated by MATLAB and generated by a Basys 2 FPGA from Digilent (Pullman, WA, USA). […]

library_books

Comparative genome analysis of the vineyard weed endophyte Pseudomonas viridiflava CDRTc14 showing selective herbicidal activity

2017
Sci Rep
PMCID: 5725424
PMID: 29229911
DOI: 10.1038/s41598-017-16495-y

[…] rity to query and e-value, bitscore, identity and length values of the hits showed in a plot for each accession. BLAST Ring Image Generator (BRIG) was used for visualisation of genome comparisons and bacterial annotation system (BASys) was used to prepare CDRTc14 circular image with annotation. […]

library_books

Comparative genomics of Lactobacillus kefiranofaciens ZW3 and related members of Lactobacillus. spp reveal adaptations to dairy and gut environments

2017
Sci Rep
PMCID: 5634458
PMID: 28993659
DOI: 10.1038/s41598-017-12916-0

[…] The ZW3 genome was re-annotated using the RAST and Basys platforms and verified using the Gene PRIMP system. After manual curation, we obtained credible genome-wide sequence annotation information (Fig. ). The genomic length of the Lb. kefiranofaciens […]

call_split

Draft Genome Sequence of Pantoea agglomerans JM1, a Strain Isolated from Soil Polluted by Industrial Production of Beta Lactam Antibiotics That Exhibits Valacyclovir Like Hydrolase Activity

2017
Genome Announc
PMCID: 5609407
PMID: 28935728
DOI: 10.1128/genomeA.00921-17
call_split See protocol

[…] eotide polymorphisms in corresponding regions were found. The genome size of Pantoea agglomerans JM1 was 4,794,872 bp in 34 scaffolds with an overall G+C content 55.14%. We predicted 4,728 genes with BASys (), 8 rRNAs with the WebMGA prediction server (), and 71 tRNAs (3 pseudo) with tRNAscan-SE (). Plasmids pPag1 and pPag3 (unlocalized in one scaffold) were identified as being closely related to […]

library_books

Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

2017
Microb Genom
PMCID: 5643016
PMID: 29114402
DOI: 10.1099/mgen.0.000123

[…] al. In order to annotate ISs, we designed our own annotation pipeline. Because IS elements in the original GenBank files were rather disparately annotated, we relied on automated annotations from the Basys annotation server []. Basys identified 11 families of IS transposase proteins (see Table S2 and Fig. S2). For each of these families, we produced a multiple alignment of their annotated sequence […]

call_split

Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat

2017
Genom Data
PMCID: 5485554
PMID: 28702355
DOI: 10.1016/j.gdata.2017.06.006
call_split See protocol

[…] sembled using CLC Genomic Workbench 5. The final whole genome assembly size was reported is 7,13,204 bp. The genome annotation was performed using RAST (Rapid Annotation using Subsystem Technology) , BASys (a web server for automated bacterial genome annotation) and MaGe (Microscope Genome Annotation) . The RAST analysis revealed total 1691 coding sequences (). A total of 1009 subsystems were ide […]

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BASys institution(s)
Departments of Biological Sciences and Computing Science, University of Alberta Edmonton, AB, Canada
BASys funding source(s)
Funding for this project was provided by the AICML, the Protein Engineering Network Centres of Excellence (PENCE Inc.) and Genome Prairie (a division of Genome Canada).

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