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401por Haas, Brian J., Dobin, Alexander, Li, Bo, Stransky, Nicolas, Pochet, Nathalie, Regev, Aviv“…RESULTS: We benchmark 23 different methods including applications we develop, STAR-Fusion and TrinityFusion, leveraging both simulated and real RNA-seq. …”
Publicado 2019
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402por Mary Mathew, K., Reshma, Renjanan, Geethu, M., Rithin, Varghese, Sabu, K.K., Nadiya, F., Noushad, Muhammad Ali, Dharan, Soumya S., Rao, Y.S., Remashree, A.B.“…The raw reads were quality filtered and assembled using TRINITY de novo assembler which created 1,11,495 (control) and 91,096 (diseased) contigs with N50 values 3013 (control) and 2729 (stressed). …”
Publicado 2019
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403“…The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. …”
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404por Klein, Ashwil, Husselmann, Lizex H. H., Williams, Achmat, Bell, Liam, Cooper, Bret, Ragar, Brent, Tabb, David L.“…Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity “genes” varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. …”
Publicado 2021
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405por Fulloon, J. D.“…By evoking imagery of the Black Death in her explanation of the Passion and the existence of suffering, Julian of Norwich sought to restore unity to medieval English society through a re-envisioning of the Holy Trinity as Earthly authority figures: family/household, Holy Mother Church, and feudal lord.…”
Publicado 2021
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406“…For example, the accuracy on the TRINITY site is more than 5% higher than that of the comparison method, which clearly proves that the presented approach achieves a better generalization performance than the compared methods.…”
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407“…We used transcriptomic sequences from 15 maize libraries assembled by Trinity and Hisat2/StringTie to demonstrate the application of the ICAnnoLncRNA pipeline.…”
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408“…It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers. Availability and implementation: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/ Contact: dzerbino@ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.…”
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409“…These accomplishments are basically predicated in the trinity of multimodality, standardization and sharing. …”
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410“…Transcript assembly using Trinity and orthology determination using HaMStR yielded 839 orthologous groups for analysis. …”
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411por Xu, Dongdong, Shen, Kang-Ning, Fan, Zhaofei, Huang, Wei, You, Feng, Lou, Bao, Hsiao, Chung-Der“…A total of 40,004,378 (NCBI SRA database SRX1406649) and 53,108,992 (NCBI SRA database SRX1406648) high quality reads were obtained from testis and ovary RNA sequencing, respectively, and 60,421 contigs (with average length of 1301 bp) were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 14,036 contigs that show gender-enriched expressional profile with either testis-enriched (237 contigs) or ovary-enriched (581 contigs) with RPKM > 100. …”
Publicado 2016
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412por Lü, Zhenming, Liu, Wan, Liu, Liqin, Shi, Huilai, Ping, Hongling, Wang, Tianming, Chi, Changfeng, Wu, Changwen, Chen, Ching-Hung, Shen, Kang-Ning, Hsiao, Chung-Der“…A total of 53,116,650 and 53,446,640 reads were obtained from the immature and matured ovaries, respectively (NCBI SRA database SRX1409472 and SRX1409473), and 70,039 contigs (N50 = 1443 bp) were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 47,288 contigs show differential expression profile and 793 contigs are highly expressed in the immature ovary, while 38 contigs are highly expressed in the mature ovary with FPKM > 100. …”
Publicado 2015
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413“…A total of 57,509,280 clean reads (deposited in NCBI SRA database with accession number of SRX1674471) were obtained from RNA sequencing and 26,811 unigenes (with N50 of 1033 bp) were obtained after de novo assembling with Trinity software. BLASTX against NR, GO, KEGG and eggNOG databases show 100%, 49%, 31% and 96% annotation rate, respectively. …”
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414por Amini, Safoora, Alias, Halimah, Aizat-Juhari, Mohd Afiq, Mat-Isa, Mohd-Noor, Adam, Jumaat Haji, Goh, Hoe-Han, Wan, Kiew-Lian“…De novo assembly of these sequences using Trinity resulted in 89,690 unique transcripts with an N50 of 1653 bp. …”
Publicado 2017
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415“…In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively. …”
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416por Roy, Neha Samir, Kim, Jung-A, Choi, Ah-Young, Ban, Yong-Wook, Park, Nam-Il, Park, Kyong-Cheul, Yang, Hee-sun, Choi, Ik-Young, Kim, Soonok“…We obtained 51,133 unigenes from transcriptome sequencing by de novo assembly using Trinity v2.1.1, TransDecoder v2.0.1, and CD-HIT v4.6 software. …”
Publicado 2018
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417“…Ancient Greece was the cradle of the Mediterranean food tradition, characterized by the Mediterranean “eternal trinity” wheat - olive oil - wine, the very essence of the country’s traditional agricultural and dietary regime, enriched by a culture of sharing and commensality. …”
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418“…The existing evaluation system of cultivated land quality mainly considers the natural quality and utilisation conditions, but without sufficient emphasis on ecological environment, which can’t meet the requirements of the trinity pattern protection policy. This study, using GIS spatial analysis and multifactor comprehensive evaluation method, constructed a comprehensive evaluation index system, and applied it in Shengzhou. …”
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419“…Expression profiles of sucrose synthase, sucrose phosphate synthase, neutral invertase, and acidic invertase/β-fructofuranosidase, as analyzed by Avadis and Trinity, showed that both analyses were complementary and consistent. …”
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420“…We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. …”
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