“…Approximately 70 million clean pair-end reads were obtained and used for de novo assembly by Trinity program, which generated 68,086 unigenes with an average length of 576 bp. …”
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“…METHODOLOGY/PRINCIPAL FINDING: We generated transcriptome of female antennae of G.molesta using the next-generation sequencing technique, and assembled transcripts from RNA-seq reads using Trinity, SOAPdenovo-trans and Abyss-trans assemblers. …”
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“…Here, we sequenced the mRNA transcriptome of pokeweed in the presence and absence of jasmonic acid (JA), a hormone mediating plant defense. Trinity-based de novo assembly of mRNA from leaf tissue and BLASTx homology searches against public sequence databases resulted in the annotation of 59 096 transcripts. …”
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“…Forty-eight simple sequence repeat (SSR) and 48 low-copy nuclear (LCN) markers were developed and validated with Fluidigm microfluidic PCR and Illumina MiSeq amplicon sequencing on 48 different individuals each. RESULTS: Individual Trinity assemblies were similar regarding annotated transcripts (13,009–14,271), mean contig length (635–742 bp), N50 value (916–1133 bp), E90N50 value (1099–1308 bp), contigs with positive BLAST hits (42–63%), and gene ontology terms. …”
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“…We performed RNA sequencing for A. ansorgei whole retina to a depth of 321 million pairs of reads and assembled 400,584 Trinity transcripts. Transcriptome-wide analyses and annotations suggest that our data set confers nearly full length coverage for the majority of retinal transcripts. …”
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“…Variables related to the functional status, frequency of complaints, and test socket satisfaction were investigated in the 2 groups. The Trinity Amputation and Prosthesis Experience Scales (TAPES) and Beck Depression Inventory (BDI) were used to assess the level of patient satisfaction with their prosthesis. …”
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“…We demonstrate the use of PIRSitePredict for functional annotation of de novo assembled genome/transcriptome by annotating uncharacterized proteins from Trinity RNA-seq assembly of embryonic transcriptomes of the following three cartilaginous fishes: Leucoraja erinacea (Little Skate), Scyliorhinus canicula (Small-spotted Catshark) and Callorhinchus milii (Elephant Shark). …”
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“…After filtration, we obtained 53,047,718 clean reads and subjected them to de novo assembly using Trinity software. Finally, we annotated 73,264 unigenes and predicted a total of 34,298 protein coding sequences. …”
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“…Our study is accompanied by a comprehensive and extensible Electronic Supplement that summarizes all data sets, assembly execution instructions, and evaluation results. Trinity, SPAdes, and Trans-ABySS, followed by Bridger and SOAPdenovo-Trans, generally outperformed the other tools compared. …”
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“…Patients's body image perception and compliance with the prosthesis paramaters were evaluated with Amputee Body Image Scale (ABIS) and Trinity Amputation and Prosthesis Experience Scales (TAPES). …”
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“…The remaining taxa occur mainly along and inland from the coast from the vicinity of the Russian River and Lake Berryessa/Putah Creek, north to the vicinity of the Smith River near the Oregon border and more inland along the Klamath and Trinity Rivers and tributaries into Oregon. The northern segment of this nearly continuous range is named Aneides klamathensis Reilly and Wake 2019. …”
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“…Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. …”
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“…The transcriptomes were assembled de novo, using Trinity, from raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). …”
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“…In this study, we performed de novo transcriptome assembly of brain tissues from Nothobranchius guentheri using Trinity. Annotation of 104,271 potential genes (with transcripts longer than 500 bp) was carried out; for 24,967 genes (53,654 transcripts), in which at least one GO annotation was derived. …”
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“…Here we investigate numerically the phase transition of a simple model system composed of anisotropic molecules, and report on our discovery of multistep nucleation of nuclei with layered positional ordering (smectic ordering), from a fluid-like nematic phase with orientational order only (no positional order). A trinity of molecular dynamics simulation, machine learning, and molecular cluster analysis yielding free energy landscapes unambiguously demonstrates the dynamics of multistep nucleation process involving characteristic metastable clusters that precede supercritical smectic nuclei and cannot be accounted for by the classical nucleation theory. …”
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“…Clinical and policy interventions should focus on specific symptoms that increased including trouble concentrating and anxiety. FUNDING: Trinity College of Arts & Sciences and Social Science Research Institute at Duke University.…”
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“…After high-throughput sequencing, Trinity software was applied for de novo assembly and the resultant 49934 unigenes were subjected for expression analysis and annotation against NR, KEGG, UniProt, and Pfam databases. …”
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“…This approach implements several de novo assemblers: Trinity, Trans-ABySS and rnaSPAdes. Several assembly metrics were examined: the percentage of reference transcripts observed in the assemblies, the percentage of RNA-seq reads involved, and BUSCO scores. …”
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“…Obtained RNA reads were assembled by Trinity assembler and 95141, 62123, 61836 contigs were identified with N50 values of 2409, 2801 and 2827 respectively. …”
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“…Satisfaction with the prosthesis was measured using the Trinity Amputation and Prosthetic Experience Scales and purposefully designed 7-point Likert scales. …”
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