Figure 1

Terminology adopted by ConiferEST with examples. Panel A: Illustration of the expected structures of cDNA library constructs as interpreted in ConiferEST. 5' terminus in SS (5TSS): → GAATTC(EcoRI) + GGCACGAGG(Adapter1) →. 3' terminus in SS (3TSS): → PolyA + CTCGAG(XhoI) →. 5' terminus in NS (5TNS): → CTCGAG(XhoI) + PolyT →. 3' terminus in NS (3TNS): → CCTCGTGCC(Adapter1) + GAATTC(EcoRI) →. SS stands for sense strand and NS for non-sense strand. Panel B: An example of a 3'-end EST sequence that fits the expected structures. FLD1_42_B03.b1_A029 is a 3'-end sequence showing a complete cDNA insert flanked by vector sequence at each end. The zoomable bar graph represents the Phred quality profile for each nucleotide base. The dark black text/bar indicates base calls within a good quality region determined using moving windows and a threshold of Phred quality value 16, whereas light black text/bar indicates calls of lower quality. PolyA/T tails are shown in green. Dark blue is used to highlight vector sequence in a good quality region, while light blue indicates vector sequence of lower quality. Sequence consistent with Adapter1 is highlighted in pink. Restriction endonuclease recognition sites for EcoRI and XhoI are brown with yellow background and brown with green background, respectively. Panel C: Two types of "double-termini assembly" (i.e., "double-termini adapters" and "double-termini polyA/T") that might result in chimeric sequences. Panel D: A supposed 3'-end sequence (COLD1_32_H06.b1_A029) is actually a 5'-end sequence, with "double-termini adapters" and "double-termini polyA/T" at each end.