%0 Journal Article %T Methodology optimizing SAGE library tag-to-gene mapping: application to Leishmania. %+ Institut Pasteur de Tunis %A Smandi, Sondos %A Guerfali, Fatma Z. %A Farhat, Mohamed %A Ben-Aissa, Khadija %A Laouini, Dhafer %A Guizani-Tabbane, Lamia %A Dellagi, Koussay %A Benkahla, Alia %Z This work was done with the support of UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (the project identifier being A50967) and with the support of the EC Framework Program VII, Project: LEISHDRUG, Grant Agreement No 223414. %< avec comité de lecture %@ 1756-0500 %J BMC Research Notes %I BioMed Central %V 5 %P 74 %8 2012 %D 2012 %R 10.1186/1756-0500-5-74 %M 22283878 %Z Life Sciences [q-bio]/Microbiology and ParasitologyJournal articles %X Leishmaniasis are widespread parasitic-diseases with an urgent need for more active and less toxic drugs and for effective vaccines. Understanding the biology of the parasite especially in the context of host parasite interaction is a crucial step towards such improvements in therapy and control. Several experimental approaches including SAGE (Serial analysis of gene expression) have been developed in order to investigate the parasite transcriptome organisation and plasticity. Usual SAGE tag-to-gene mapping techniques are inadequate because almost all tags are normally located in the 3'-UTR outside the CDS, whereas most information available for Leishmania transcripts is restricted to the CDS predictions. The aim of this work is to optimize a SAGE libraries tag-to-gene mapping technique and to show how this development improves the understanding of Leishmania transcriptome. FINDINGS: The in silico method implemented herein was based on mapping the tags to Leishmania genome using BLAST then mapping the tags to their gene using a data-driven probability distribution. This optimized tag-to-gene mappings improved the knowledge of Leishmania genome structure and transcription. It allowed analyzing the expression of a maximal number of Leishmania genes, the delimitation of the 3' UTR of 478 genes and the identification of biological processes that are differentially modulated during the promastigote to amastigote differentiation. CONCLUSION: The developed method optimizes the assignment of SAGE tags in trypanosomatidae genomes as well as in any genome having polycistronic transcription and small intergenic regions. %G English %Z WHO Collaborating Center for Research and Training in Leishmaniasis %2 https://riip.hal.science/pasteur-00681569/document %2 https://riip.hal.science/pasteur-00681569/file/Smandi-1756-0500-5-74.pdf %L pasteur-00681569 %U https://riip.hal.science/pasteur-00681569 %~ RIIP %~ RIIP_TUNIS