title: Methodology optimizing SAGE library tag-to-gene mapping: application to Leishmania.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratoire d'Immuno-Pathologie, Vaccinologie et Génétique Moléculaire (LIVGM), WHO Collaborating Center for Research and Training in Leishmaniasis, Institut Pasteur de Tunis, 13 place Pasteur BP74 1002, Tunis, Tunisia. alia.benkahla@pasteur.rns.tn.
authors.forename: Sondos
authors.initials: S
authors.lastname: Smandi
authors.forename: Fatma Z
authors.initials: FZ
authors.lastname: Guerfali
authors.forename: Mohamed
authors.initials: M
authors.lastname: Farhat
authors.forename: Khadija
authors.initials: K
authors.lastname: Ben-Aissa
authors.forename: Dhafer
authors.initials: D
authors.lastname: Laouini
authors.forename: Lamia
authors.initials: L
authors.lastname: Guizani-Tabbane
authors.forename: Koussay
authors.initials: K
authors.lastname: Dellagi
authors.forename: Alia
authors.initials: A
authors.lastname: Benkahla