Sentence examples for using the trinity assembly from inspiring English sources
These were assembled into 115,739 putatively unique transcripts (PUTs) using the Trinity assembly program (Grabherr et al., 2011) and compared with the 4 September 2013 version of NCBI NR using Blastx (Altschul et al., 1997).
We obtained 120,426 contigs (≥200 bp) using the Trinity assembly software.
Therefore, we used the results obtained using the Trinity assembly for further biological interpretation and functional analysis.
This analysis revealed no significant differences using the Trinity assembly and only three significant differences with the Velvet assembly.
The de novo assembly of the quality processed reads using the Trinity assembly program resulted in 209,654 transcript isoforms.
Furthermore, there was a lower degree of redundancy in the list of annotated differentially expressed transcripts identified using the Trinity assembly.
We therefore elected to use the Trinity assembly to retain maximum information for further transcript analysis and the Trinity assembly is also available in Additional file 5.> To validate and annotate the assembled unigenes, the 16,798 unigenes generated by Trinity were subjected to BLASTX searches (E-value ≤ 1e-5) against public protein databases.
Using the Trinity transcriptome-assembly software, a total of 120,426 assembled transcripts were obtained from seven sample libraries (untreated control, defoliation, and simulated grazing).
We obtained 108,502 assembled unigenes using the Trinity de novo assembly method and identified numerous potential cold sensing transcription factor genes and various key signal transduction components at the transcriptome level.
We got 54,870 assembled unigenes using the Trinity de novo assembly method, and a number of chilling regulated genes were identified, providing useful resources for gene mining to improve cold tolerance of plants.
Using the Trinity de novo assembly program [ 28], all clean reads were assembled into 31,838 transcripts, with an N50 length of 956 bp and an average length of 657 bp (Additional file 1: Table S1).
