BLAST+: architecture and applications

Camacho, Christiam; Coulouris, George; Avagyan, Vahram; Ma, Ning; Papadopoulos, Jason S.; Bealer, Kevin; Madden, Thomas

doi:10.1186/1471-2105-10-421

Cited by 16,681 publications

(14,738 citation statements)

References 16 publications

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“…(2016, 2018). BLAST searches were performed using the blastn command of the ncbi‐blast‐2.2.30+ software (Camacho et al ., 2009). Synteny of the QTL between IPO323, 3D1, 3D7, 1E4 and 1A5 was analysed using blastn and visualised using the R package geno P lot R v.0.8.4 (Guy et al ., 2010).…”

Section: Methodsmentioning

confidence: 99%

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

et al. 2018

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Summary Cultivar‐strain specificity in the wheat–Zymoseptoria tritici pathosystem determines the infection outcome and is controlled by resistance genes on the host side, many of which have been identified. On the pathogen side, however, the molecular determinants of specificity remain largely unknown.We used genetic mapping, targeted gene disruption and allele swapping to characterise the recognition of the new avirulence factor Avr3D1. We then combined population genetic and comparative genomic analyses to characterise the evolutionary trajectory of Avr3D1.Avr3D1 is specifically recognised by wheat cultivars harbouring the Stb7 resistance gene, triggering a strong defence response without preventing pathogen infection and reproduction. Avr3D1 resides in a cluster of putative effector genes located in a genome region populated by independent transposable element insertions. The gene was present in all 132 investigated strains and is highly polymorphic, with 30 different protein variants identified. We demonstrated that specific amino acid substitutions in Avr3D1 led to evasion of recognition.These results demonstrate that quantitative resistance and gene‐for‐gene interactions are not mutually exclusive. Localising avirulence genes in highly plastic genomic regions probably facilitates accelerated evolution that enables escape from recognition by resistance proteins.

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Section: Methodsmentioning

confidence: 99%

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

et al. 2018

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“…In Allora, all PDBs belonging to the same UniProt or GenBank entries are connected. BLAST+ (Camacho et al , 2009) was used to search for the most similar UniProt/GenBank protein sequence compared to the human proteins containing MXEs. The hit with the lowest E‐value was taken, and the associated PDB chains were aligned to the human protein using m‐coffee (Wallace et al , 2006).…”

Section: Methodsmentioning

confidence: 99%

The landscape of human mutually exclusive splicing

Hatje

Rahman

Vidal

et al. 2017

Molecular Systems Biology

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Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.

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“…Galaxy, a python script [47], was used to perform reciprocal protein BLAST searches (NCBI BLAST+ v. 2.3.0 [48]. Default parameters (minimum percentage identity: 70%; minimum High Scoring Pair (HSP) coverage: 50%) were used and all redundancies were removed.…”

Section: Methodsmentioning

confidence: 99%

An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae

et al. 2018

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The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species E. cloacae, K. pneumoniae and E. coli emerged from their common ancestry. A representative MGI from E. cloacae was named MIR17-GI, because it harbors the novel β-lactamase gene variant blaMIR17. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective E. cloacae isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst Enterobacteriaceae. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections.

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BLAST+: architecture and applications

Cited by 16,681 publications

References 16 publications

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

The landscape of human mutually exclusive splicing

An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae

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