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For example, RAD tags can be sequenced to discover and map SNPs [10].
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Next-generation sequencing (NGS) technologies have been recently used for whole genome sequencing and for re-sequencing projects where the genomes of several specimens are sequenced to discover large numbers of single nucleotide polymorphisms (SNPs) for exploring within-species diversity, constructing haplotype maps and performing genome-wide association studies (GWAS) [13].
Finally, in the marker validation phase, additional samples are sequenced to confirm the discovered markers.
A total of 384 X-linked alleles of the miRNA genes were sequenced in order to discover multiple rare alleles.
Three approaches were employed for input sequences to discover motifs among multiple sequences [ 20].
Large numbers of ESTs have been sequenced and analysed in pine to discover wood formation and wood quality trait related genes [ 30- 33].
Tumor DNA was sequenced and no mutation was discovered in EGFR, KRAS, BRAF, KIT, and PDGFRA.
Interestingly, this is a serious research question, for, if it were answered, molecular biologists engaged in genomic sequencing would be able to discover the genes in their sequence data far more rapidly than they are now able to do.
A new aspect of this approach is to discover sequence polymorphisms in cultivars or variants of species, where one of them has been sequenced but where no sequence information is yet available from the other ones.
While EST sequencing can be used to discover genic microsatellites, direct screening of cDNA libraries for repeat motifs can save on overall sequencing costs.
Publically available Expressed Sequence Tag (EST) sequences were used to discover isoforms of messenger RNA [ 24, 54, 55].
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