@article{fdi:010060556,
  title = {{A}n improved method for {TAL} effectors {DNA}-binding sites prediction reveals functional convergence in {TAL} repertoires of {X}anthomonas oryzae strains},
  author = {{P}erez-{Q}uintero, {A}. {L}. and {R}odriguez, {L}. {M}. and {D}ereeper, {A}lexis and {L}opez, {C}. and {K}oebnik, {R}alf and {S}zurek, {B}oris and {C}unnac, {S}{\'e}bastien},
  editor = {},
  language = {{ENG}},
  abstract = {{T}ranscription {A}ctivators-{L}ike {E}ffectors ({TALE}s) belong to a family of virulence proteins from the {X}anthomonas genus of bacterial plant pathogens that are translocated into the plant cell. {I}n the nucleus, {TALE}s act as transcription factors inducing the expression of susceptibility genes. {A} code for {TALE}-{DNA} binding specificity and high-resolution three-dimensional structures of {TALE}-{DNA} complexes were recently reported. {A}ccurate prediction of {TAL} {E}ffector {B}inding {E}lements ({EBE}s) is essential to elucidate the biological functions of the many sequenced {TALE}s as well as for robust design of artificial {TALE} {DNA}-binding domains in biotechnological applications. {I}n this work a program with improved {EBE} prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of {TALE}-{DNA} interactions. {T}o gain a systems perspective on the large {TALE} repertoires from {X}. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. {I}ntegrating predictions and available expression data in a {TALE}-gene network revealed multiple candidate transcriptional targets for many {TALE}s as well as several possible instances of functional convergence among {TALE}s.},
  keywords = {},
  booktitle = {},
  journal = {{P}los {O}ne},
  volume = {8},
  numero = {7},
  pages = {e68464},
  ISSN = {1932-6203},
  year = {2013},
  DOI = {10.1371/journal.pone.0068464},
  URL = {https://www.documentation.ird.fr/hor/fdi:010060556},
}