CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing

Ramos, Ravi José Tristão; Martins, Allan Cézar de Azevedo; Delgado, Gabrielle da Silva; Ionescu, Crina-Maria; Ürményi, Turán P.; Silva, Rosane; Koča, Jaroslav

doi:10.1093/bioinformatics/btx465

Cited by 2 publications

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“…In the first step, genes were deduplicated using CD-hit [ 52 ] to reduce the enormous number of sequences. Then, gene pairs with at least some local sequence similarity were identified using an optimized implementation of the Blast alignment tool [ 42 ], called CrocoBLAST [ 53 ] (used parameters blastp -max_target_seqs 1,000,000 -max_hsps 1. All other parameters are default).…”

Section: Methodsmentioning

confidence: 99%

PHERI—Phage Host ExploRation Pipeline

et al. 2023

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Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages’ host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection.

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Section: Methodsmentioning

confidence: 99%

PHERI—Phage Host ExploRation Pipeline

et al. 2023

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“…In the first step, genes were deduplicated using CD-hit [52] to reduce the enormous number of sequences. Then, gene pairs with at least some local sequence similarity were identified using an optimized implementation of the Blast alignment tool [53], called CrocoBLAST [54]. Afterwards, the identified pairs with high local sequence similarity underwent thorough pairwise alignment [55] to retrieve more accurate similarity scores.…”

Section: Methodsmentioning

confidence: 99%

PHERI - Phage Host Exploration pipeline

Baláž

Kajsik

Budiš

et al. 2020

Preprint

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Antibiotic resistance is becoming a common problem in health care, veterinary medicine, agriculture or food industry. Multi-resistant bacterial strains occur in all regions of the world. One of the possible future solutions is the use of bacteriophages in therapy.Bacteriophages are the most abundant form of life in the biosphere, so it is highly likely that we can purify a specific phage against each target bacterium. A standard identification and consistent characterization of individual bacteriophages include host-specificity of viruses.Unfortunately, these routine methods are also considerably time consuming. With the advent of new modern sequencing methods, scientists are able to obtain multiple phage sequences from samples and identify more phages. However there appeared a problem with unknown host specificity of identified phages. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable to determine a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm based tool called PHERI. PHERI predicts suitable bacterial host genus for purification of individual viruses from different samples. In addition, the tool can identify and highlight protein sequences that are important for host selection.

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CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 2 publications

References 7 publications

PHERI—Phage Host ExploRation Pipeline

PHERI—Phage Host ExploRation Pipeline

PHERI - Phage Host Exploration pipeline

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