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ARTADE2 is superior to ARTADE1 with regard to both end and transcript structure predictions.
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The data consisted of responses from two questionnaires, one applied at the beginning of the course and one at the end, and transcripts from all the courses.
Since splice dinucleotides occur at both ends of introns, transcript sequences do not contain splice dinucleotides.
End-to-end transcript levels were quantified with the aid of a Fuji phosphorimager (and Aida software).
We carried out sequencing of both the whole transcriptome and transcript 5′ ends from the filamentous fungus A. nidulans using five different growth conditions.
Both showed the same decreasing trend of probe intensity near 3' end and 5' end of transcripts (See Figure 1 for more details).
Let 0 and L (base pair, bp) be the positions of 3' end and 5' end of a transcript before amplification, where L is the length of the transcript.
Therefore the DeTCT output specifies the distance between the TC 3′ end and the nearest Ensembl transcript 3′ end on the same strand.
We identified the 5′- and 3′-boundaries of transcripts by searching for a sharp decline of RNA-Seq reads signals at both ends of the annotated transcripts.
TEX specifically degrades RNAs with a 5' P end but does not degrade transcripts with a 5' PPP end and therefore enriches for primary transcripts.
Therefore, both ends of the mapped transcripts were extended so that predicted CDSs contained the start and the stop codons.
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