BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

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A Digital Pathology Solution to Resolve the Tissue Floater Conundrum

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2020-0034-oa ◽

2020 ◽

Author(s):

Liron Pantanowitz ◽

Pamela Michelow ◽

Scott Hazelhurst ◽

Shivam Kalra ◽

Charles Choi ◽

...

Keyword(s):

Digital Pathology ◽

Primary Diagnosis ◽

Image Search ◽

Molecular Tests ◽

Tissue Identification ◽

Digital Database ◽

Glass Slides ◽

Search Tool ◽

Hematoxylin And Eosin ◽

Whole Slide Images

Context.— Pathologists may encounter extraneous pieces of tissue (tissue floaters) on glass slides because of specimen cross-contamination. Troubleshooting this problem, including performing molecular tests for tissue identification if available, is time consuming and often does not satisfactorily resolve the problem. Objective.— To demonstrate the feasibility of using an image search tool to resolve the tissue floater conundrum. Design.— A glass slide was produced containing 2 separate hematoxylin and eosin (H&E)-stained tissue floaters. This fabricated slide was digitized along with the 2 slides containing the original tumors used to create these floaters. These slides were then embedded into a dataset of 2325 whole slide images comprising a wide variety of H&E stained diagnostic entities. Digital slides were broken up into patches and the patch features converted into barcodes for indexing and easy retrieval. A deep learning-based image search tool was employed to extract features from patches via barcodes, hence enabling image matching to each tissue floater. Results.— There was a very high likelihood of finding a correct tumor match for the queried tissue floater when searching the digital database. Search results repeatedly yielded a correct match within the top 3 retrieved images. The retrieval accuracy improved when greater proportions of the floater were selected. The time to run a search was completed within several milliseconds. Conclusions.— Using an image search tool offers pathologists an additional method to rapidly resolve the tissue floater conundrum, especially for those laboratories that have transitioned to going fully digital for primary diagnosis.

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Development of specific primers for Fusarium oxysporum causing damping off of Lilium formolongi

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-019-0015-2 ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Takeshi Toda ◽

Shun Hanesaka ◽

Kuniaki Shishido ◽

Shin-ichi Fuji ◽

Hiromitsu Furuya

Keyword(s):

Fusarium Oxysporum ◽

Pathogenic Fungus ◽

Primer Design ◽

Damping Off ◽

Specific Primers ◽

Forma Specialis

AbstractPrimers specific for the hypothetical forma specialis of Fusarium oxysporum were designed to amplify DNA from this pathogenic fungus that infects plants including lilies. The F. oxysporum sequence between the transposal elements han and hop was used for primer design. Three primer pairs designed from this region were confirmed as specific for 24 isolates of F. oxysporum pathogenic to lilies, except for one pathogenic isolates as extraordinary. No amplification was observed from F. oxysporum non-pathogenic to lily, from 12 forma specialis, and 14 fungi and oomycetes concerned with Liliaceae plants. We propose that specific primers designed from this region will be useful to detect isolates of F. oxysporum that are pathogenic to lilies.

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Identification of Bloodmeals from Sand Flies (Diptera: Psychodidae) Collected in the Parque Nacional do Viruá, State of Roraima, Brazil

Journal of Medical Entomology ◽

10.1093/jme/tjab068 ◽

2021 ◽

Author(s):

Bruno Leite Rodrigues ◽

Glaucilene da Silva Costa ◽

Paloma Helena Fernandes Shimabukuro

Keyword(s):

Blood Feeding ◽

Sand Flies ◽

Feeding Preferences ◽

Light Traps ◽

Dasypus Novemcinctus ◽

Search Tool ◽

Vertebrate Hosts ◽

Host Blood ◽

Clustering Pattern ◽

Species Being

Abstract The transmission of pathogens that cause leishmaniases occurs by the bite of female sand flies (Diptera: Psychodidae) in their vertebrate hosts, which makes the identification of their bloodmeal sources an important step for the control and epidemiology of these diseases. In Brazil, the state of Roraima has a great diversity of sand flies, vertebrate hosts, and protozoan Leishmania, but little is known about the host blood-feeding preferences of sand flies. Thus, we evaluated the bloodmeal sources of sand flies collected from their sylvatic habitats in Parque Nacional do Viruá, Roraima. Fieldwork was carried-out between 13th and 18th August 2019 using CDC light traps. Sand flies were slide-mounted and morphologically identified using the head and last segments of the abdomen. Engorged females had their DNA extracted, followed by amplification and sequencing of the cytochrome b (cytb) molecular marker for vertebrates. Sequences were analyzed and compared with those from GenBank using the BLASTn search tool, in addition to the reconstruction of a phylogenetic tree to demonstrate the clustering pattern of these sequences. A total of 1,209 sand flies were identified, comprising 20 species, in which the most abundant were Psychodopygus ayrozai (Barretto and Coutinho) (42.10%) and Psychodopygus chagasi (Costa Lima) (26.22%). Bloodmeal source identification was successfully performed for 34 sand flies, that confirm four vertebrate species, being the most abundant the armadillo Dasypus novemcinctus Linnaeus, 1758 (Cingulata: Dasypodidae).

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GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments

BMC Bioinformatics ◽

10.1186/s12859-021-04133-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jeongmin Bae ◽

Hajin Jeon ◽

Min-Soo Kim

Keyword(s):

Data Structures ◽

Primer Design ◽

Main Memory ◽

Design Tools ◽

Workload Balancing ◽

Qpcr Analysis ◽

Computational Speed ◽

Entire Sequence ◽

Target Sequences ◽

Coalesced Memory

Abstract Background Design of valid high-quality primers is essential for qPCR experiments. MRPrimer is a powerful pipeline based on MapReduce that combines both primer design for target sequences and homology tests on off-target sequences. It takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB. Due to the effectiveness of primers designed by MRPrimer in qPCR analysis, it has been widely used for developing many online design tools and building primer databases. However, the computational speed of MRPrimer is too slow to deal with the sizes of sequence DBs growing exponentially and thus must be improved. Results We develop a fast GPU-based pipeline for primer design (GPrimer) that takes the same input and returns the same output with MRPrimer. MRPrimer consists of a total of seven MapReduce steps, among which two steps are very time-consuming. GPrimer significantly improves the speed of those two steps by exploiting the computational power of GPUs. In particular, it designs data structures for coalesced memory access in GPU and workload balancing among GPU threads and copies the data structures between main memory and GPU memory in a streaming fashion. For human RefSeq DB, GPrimer achieves a speedup of 57 times for the entire steps and a speedup of 557 times for the most time-consuming step using a single machine of 4 GPUs, compared with MRPrimer running on a cluster of six machines. Conclusions We propose a GPU-based pipeline for primer design that takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB at once without an additional step using BLAST-like tools. The software is available at https://github.com/qhtjrmin/GPrimer.git.

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