Schematic of S. salar FLcDNA contig identification and reference FLcDNA identification. Two-stage assembly of 434,384 high-quality 5'- and 3'-end ESTs identified 81,398 contigs (1-2) for FL contig identification. A BLASTX was carried out resulting in 34,451 well-annotated contigs (3), which were further reduced to 14,021 FL annotations by increasing the stringency of the local alignment length (4). In-frame annotation-flanking start and stop codons were found from the reduced set, resulting in a set of 10,026 FL contigs (5). The FL contigs represent the complete set of FL unique putative transcripts. A set of all reads and subsequently sequenced library rgf reads was mapped to the FL contigs (6). Those clones whose 5'- and 3'-end reads map to the same contig were analyzed to determine sequence overlap (complete) or non-overlap (incomplete) (7). Only complete clones are considered, and a single representative of a clone is taken for each transcript resulting in 5,953 complete reference FLcDNAs (8).