- Unité d’accueil : IBDM

- Nom de l’encadrant : Bianca Habermann

- Courriel de l’encadrant : Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir.

- Bref descriptif :
The Mexican Axolotl (Ambystoma mexicanum) has the capacity to regenerate entire body parts, such as its limbs or its tail. Therefore, it is a popular model organism for research in regenerative medicine. In order to manipulate the Axolotl genetically, we recently sequenced and assembled the Axolotl genome using PacBio and Illumina sequencing. Its genome is 10 x larger than the human genome. We have observed that intron sizes have expanded greatly in the Axolotl genome. The large introns make the correct prediction of genes difficult and even though a rich transcriptomics resource exists for Axolotl, quite a number of genes could not be correctly predicted using standard algorithms.
For this M1 stage, we propose to develop a two-step algorithm for transcriptome-based gene annotation in the Axolotl genome.  
Step1: identify the genomic region using transcript-mapping with classical techniques, such as spaln.
Step2: re-align the transcript to the identified genomic region using highly sensitive methods, such as GMAP (Wu, et al., 2005) and/or BLAST/BLAT (Altshul, et al., 1990).  

- Compétences techniques attendues (langage de programmation, outils imposés, etc.) :
Python; BLAST-suite;