BLASTatlas protocols

View BLASTatlas computational protocol

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BLASTatlas specifications

Information


Unique identifier OMICS_13422
Name BLASTatlas
Interface Application programming interface
Restrictions to use None
Input data A file containing the genome sequence, including all annotated coding sequences (comprising protein-start, -stop and -direction) for the reference genome.
Programming languages Perl
Computer skills Advanced
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for BLASTatlas

BLASTatlas in pipelines

 (2)
2015
PMCID: 4535895
PMID: 26484173
DOI: 10.1016/j.gdata.2015.01.006

[…] p. chlororaphis may share a more recent common ancestor with p. fluorescens than with p. syringae., conserved and specific regions in the genome can be identified through global alignments. blastatlas gives an overview of the whole genome homology, and the reference genome can be compared at the gene and/or protein level against many genomes . in this study, the reference genome of ht66 […]

2009
PMCID: 2777879
PMID: 19860885
DOI: 10.1186/1471-2148-9-258

[…] are in bold. +vibrio angustum and vibrio fischeri were reclassified as photobacterium angustum [] and aliivibrio fischeri [], respectively. *calculated using concatenated chromosome sequences., the blastatlas plots were constructed as described previously [,]. the pangenome plot, and proteome matrix were constructed as described []. for building the atlas, the genomes were automatically […]


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BLASTatlas in publications

 (4)
PMCID: 4370579
PMID: 25799515
DOI: 10.1371/journal.pone.0120659

[…] these sequenced strains is shown in . to identify specific regions in yn4–84, yn4–84 was compared with yn1–91 using mauve []. gview was used to determine the core genomes of the analyzed strains. blastatlas was used to identify variable genome regions based on a comparison of yn4–84 with an additional forty-six genomes []. blast parameters were set as follows: expected cutoff value 1e-10, […]

PMCID: 4342571
PMID: 25721465
DOI: 10.1038/srep08642

[…] such as an overview of genomic conserved regions, orthologous group categorization, and orthologous relationship analysis, were performed in order to identify conserved and strain-specific cdss. blastatlas tool was used to compare the genomes of the seven arthrobacter strains and to provide a quick overview of the conserved genomic regions (). the genome of tc1 was used as a reference […]

PMCID: 3091793
PMID: 21143895
DOI: 10.1186/1471-2164-11-698

[…] (f1: bacterial response to iron deficiency versus control) and serotype (f2 response between serotypes 1, 2, 3, 5, 6 and 7) and the combined effect of treatment and serotype (f1:f2)., the program blastatlas http://www.cbs.dtu.dk/ws/blastatlas, was used for mapping and visualizing whole genome homology of expressed genes []. using the published genome of a. pleuropneumoniae serotype 3 str. […]

PMCID: 2443382
PMID: 18522759
DOI: 10.1186/1471-2164-9-271

[…] of the genome of a. caulinodans strain ors571 (hereafter designated a. caulinodans) revealed a single circular chromosome of 5,369,772 base pairs []. relevant genome features generated with the blastatlas tool [] are presented in figure and can be viewed in detail as a web-based resource []. the putative origin of replication was predicted based on the position of a gc skew shift (figure ) […]


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BLASTatlas institution(s)
Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark
BLASTatlas funding source(s)
The work was supported by a grant from the European Union through the EMBRACE network of Excellence, contract number LSHG-CT-2004-512092 and a grant from the Danish Center for Scientific Computing.

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