We downloaded all 309,976 raw Sanger ESTs for Pinus taeda from NCBI Trace Archive (http://trace.ncbi.nlm.nih.gov/Traces/trace.cgi), which were generated by three different sequencing centers or labs including previously well-known TIGR institute.
Among these down-regulated genes, Sncg (which is represented by two different sequences on the array and is 4-fold down-regulated) might be directly associated with the retinal aspects of the disease.
The Pain-1 sequences obtained from the same BAC by two different sequencing techniques (454 and Sanger sequencing) differed by a six-nucleotide insertion in intron 2. The Pain-1 gene consists of seven exons and six introns and is around 4 kbp long.
Plasmids may be integrated into the genome and thereby the plasmid sequences can be present in the assemblies surrounded by two different sequence environments (plasmid only sequences or adjacent genome parts), making the integration site a low coverage region.
Following the main reconstruction steps described in Figure 1, functional annotation of the whole genome was firstly performed by two different sequence similarity search programs.
In P. infestans, the region did not assemble continuously and is represented by segments from three different sequence contigs.
The negative sets were made by random sampling of precursors from three different sequence sets: A) the full human genome (hg18, March 06 assembly).
In order to ensure that sequences of alignment are representative and diverse, we collected the homologue sequences by using seventeen different sequences as initial query sequences.
However, in our opinion, two or more sequences from one band can contribute to the change of band intensity observed on the autoradiography, as suggested by the fact that two different sequences cloned from the same band were both confirmed to be up-regulated after pathogen attack (43DU149 and 43DU149').
This observation cannot be solely explained by the priming mechanism where two different sequences on the chromosome were joined, and can only be explained if the same sequence is present on both ends of the sequenced fragment with one version inverted (Fig. 1D).
