Leishmania genome projects involving specific species and strains are resulting in a rapid accumulation of full and partial expressed DNA sequences. Expressed sequence tags (ESTs) collected from public databases can be mined for both structural and functional genomics' motifs.

In this study we mined L. major EST that were available from the online NCBI database, for simple sequence repeats (SSRs), which can be used in the developing of simple and complex microsatellites, as well as to assess their distributions.

In this study, we acquired a total of 2,191 ESTs of the parasite species L. major expressed in both stages (amastigote and promastigote) that were mined using deterministic text search algorithms as implemented in the MISA script. After sequence reduction (joining overlapping fragments) using CAP3, we mined a total of 1448 ESTs (305 from amastigote, and 1211 from promastigote stages).

The frequencies of identified mono, di, tri, tetra, and complex SSRs are about 30%, 46%, 4%, 1%, and 19% respectively. Principal components analysis showed that the complex repeat motifs are the most abundant SSR in the amastigote stage, while the mono-repeats are the most abundant in the promastigote stage.

Comparative sequence analyses of identified and stage specific SSRs, showed that the proportion of differentially expressed fragments (after reduction) in amastigote is 54%, which is statistically lower (p-value <0.001) than those differentially expressed fragments in promastigote (about 74%). Further analysis suggests that the majority of the EST-SSRs code for signal peptides in the parasite trans-membrane region.

Furthermore, functional domain marker (FDM-SSR) analysis of these identified SSR-ESTs revealed their potential role in the leishmania metabolism. The protein PDIa is expressed in the amastigote stage only, while the EF-hand domain, the GrpE nucleotide exchange factor SHERP, 40S ribosomal protein S3, Metallo-peptidase family M24, and PQ loop repeat are all expressed in the promastigote stage only.