Sentence examples for base of transcript from inspiring English sources

Expected fragments per 1000 base of transcript per million fragments mapped (FPKM) [ 19], has been typically used to measure genes expression level from RNA-Seq data.

While gene expression varied over several orders of magnitude, the average and median expression levels were 194.2 and 31.8 FPKM (Fragments per kilo- base of transcript per million mapped reads) respectively.

Copy numbers of the 331 miRNAs identified in oyster haemocytes were counted and further converted to fragments per kilo base of transcript per million fragments mapped (FPKM) value to analyze their expression level (Additional file 6: Table S5).

RSEM (Li and Dewey 2011) was then used to generate transcript percentages and fragments per kilo bases of transcript per million mapped reads (FPKM) values for relative expression of each transcript.

It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly.

In this case, however, we not only classify the reads, but use the Tophat mappings to compute approximate levels of gene expression [measured in fragments per thousand bases of transcript per million mapped reads, or FPKM Trapnell et al. (2010)] and use human species-specific quantitative RT-PCR (qRT-PCR) on selected genes to validate the results.

To address this issue, we prepared a new NRO library from which we specifically sequenced the 3′ end bases of transcripts and found a small peak of transcription consistent with poly(A) cleavage.

In the Blast analysis two types of alignments were exploited: "exact alignment", i.e. 100% sequence identity over 25 base pairs of transcript and probe sequence, and "near-exact alignment" with at most one mismatch (identity of 24 base pairs).

The copy number and the logarithm of Fragments per kilo-base of transcripts per million mapped reads (FPKM) showed a positive correlation (Additional file 2: Figure S24).

The number of assembled transcripts, total bases of transcripts, average length of all unigenes, N50, number of long-transcripts (≥1 kb), and number of reads that could be mapped back to transcripts (RMBT) were compared to evaluate the assembly quality with different methods and select the optimum reference transcriptome for further study.

3′-UTRs are defined as the sequence between the stop codon and the last base of the transcript.