H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs

Ye, Weicai; Chen, Ying; Zhang, Yongdong; Xu, Yuesheng

doi:10.1093/bioinformatics/btw769

Cited by 22 publications

(10 citation statements)

References 35 publications

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“…Using BLAST 2.2.28+ [ 55 ], the protein sequences of the predicted genes were aligned with NCBI nr, Genes, STRING, and GO databases to obtain the gene annotation information. COG annotations (Clusters of Orthologous Groups of proteins, , accessed on 20 August 2016) were obtained by alignment with STRING (v 9.05, , accessed on 20 August 2016) database.…”

Section: Methodsmentioning

confidence: 99%

Genomic Analyses of Penicillium Species Have Revealed Patulin and Citrinin Gene Clusters and Novel Loci Involved in Oxylipin Production

Yin

Pennerman

Jurick

et al. 2021

JoF

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Blue mold of apple is caused by several different Penicillium species, among which P. expansum and P. solitum are the most frequently isolated. P. expansum is the most aggressive species, and P. solitum is very weak when infecting apple fruit during storage. In this study, we report complete genomic analyses of three different Penicillium species: P. expansum R21 and P. crustosum NJ1, isolated from stored apple fruit; and P. maximae 113, isolated in 2013 from a flooded home in New Jersey, USA, in the aftermath of Hurricane Sandy. Patulin and citrinin gene cluster analyses explained the lack of patulin production in NJ1 compared to R21 and lack of citrinin production in all three strains. A Drosophila bioassay demonstrated that volatiles emitted by P. solitum SA and P. polonicum RS1 were more toxic than those from P. expansum and P. crustosum strains (R27, R11, R21, G10, and R19). The toxicity was hypothesized to be related to production of eight-carbon oxylipins. Putative lipoxygenase genes were identified in P. expansum and P. maximae strains, but not in P. crustosum. Our data will provide a better understanding of Penicillium spp. complex secondary metabolic capabilities, especially concerning the genetic bases of mycotoxins and toxic VOCs.

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Section: Methodsmentioning

confidence: 99%

Genomic Analyses of Penicillium Species Have Revealed Patulin and Citrinin Gene Clusters and Novel Loci Involved in Oxylipin Production

Yin

Pennerman

Jurick

et al. 2021

JoF

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“…Through BLAST [16] comparison software (https://blast.ncbi.nlm.nih.gov/Blast.cgi), the unigenes sequences were compared with the protein databases NR (NCBI non-redundant protein sequences, http://www.ncbi.nlm.nih.gov/) [17] and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.ad.jp/kegg/kegg2.html) [18]. Classification information and gene function annotation were carried out by BLASTx (E-value �1.0E-05).…”

Section: Functional Annotation and Classificationmentioning

confidence: 99%

Transcriptome sequencing and screening of genes related to sex determination of Trichosanthes kirilowii Maxim

Liao

Zhang

et al. 2020

PLoS ONE

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Trichosanthes kirilowii Maxim. (TK) is a dioecious plant in the Cucurbitaceae for which different sexes have separate medicinal uses. In order to study the genes related to sex determination, transcriptome sequencing was performed on flower buds of male and female plants using the high-throughput sequencing technology. A total of 145,975 unigenes and 7110 DEGs were obtained. There were 6776 DEGs annotated to 1234 GO terms and enriched to 18 functional groups, including five biological processes related to sugar metabolism. KEGG pathway analysis indicated genes involved in hormone transduction, hormone synthesis and carbohydrate metabolism. Many DEGs of TK are involved in reproductive organ formation, hormone signal transduction and regulatory networks. Combining the results of GO, KEGG and qRT-PCR, 11 sex determining candidate genes of TK were selected, including MYB80,

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“…DIAMOND [11] constructs a double index to traverse query and reference seeds more quickly. GPU-BLAST [12], HPC-BLAST [13], and H-BLAST [14] parallelize the database search on high-performance systems.…”

Section: A Dna Sequence Interpretationmentioning

confidence: 99%

Unaligned Sequence Similarity Search Using Deep Learning

Senter¹,

Royalty

Steen

et al. 2019

2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does not have a close match in the database. In addition, each comparison can be costly when the database is large since it requires alignments and a series of string comparisons. In this work we propose a novel approach: using recurrent neural networks to embed DNA or amino-acid sequences in a lowdimensional space in which distances correlate with functional similarity. This embedding space overcomes both shortcomings of the method of aligning sequences and comparing homology. First, it allows us to obtain information about genes which do not have exact matches by measuring their similarity to other ones in the database. If our database is labeled this can provide labels for a query gene as is done in traditional methods. However, even if the database is unlabeled it allows us to find clusters and infer some characteristics of the gene population. In addition, each comparison is much faster than traditional methods since the distance metric is reduced to the Euclidean distance, and thus efficient approximate nearest neighbor algorithms can be used to find the best match. We present results showing the advantage of our algorithm. More specifically we show how our embedding can be useful for both classification tasks when our labels are known, and clustering tasks where our sequences belong to classes which have not been seen before.

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H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 22 publications

References 35 publications

Genomic Analyses of Penicillium Species Have Revealed Patulin and Citrinin Gene Clusters and Novel Loci Involved in Oxylipin Production

Genomic Analyses of Penicillium Species Have Revealed Patulin and Citrinin Gene Clusters and Novel Loci Involved in Oxylipin Production

Transcriptome sequencing and screening of genes related to sex determination of Trichosanthes kirilowii Maxim

Unaligned Sequence Similarity Search Using Deep Learning

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