322 :322 11 2010, bmc bioinformatics page 3 of 10 en
TRANSCRIPT
Técnico bioinformático en modelado 3D de RNA
RNA 3D modeling Bioinformatician
Structural Genomics Unit. CIPF. Valencia.
Buscamos licenciados en Bio*, Física, Matemáticas, Informática o similar. Nuestro grupo, que está localizado en la ciudad de Valencia, ofrece sueldos competitivos y un entorno científico excelente. Para más información sobre nuestro grupo: http://sgu.bioinfo.cipf.es.
El/La candidat@ part ic ipará en el desarrol lo y implementación de nuevos métodos de predicción de estructura de RNA usando la plataforma Integrative Modeling Platform. Este proyecto esta financiado por el MICINN y incluye un contrato inicial en pruebas que se podrá extender a un máximo de dos años y medio. El candidato tendrá la oportunidad de hacer un doctorado en Bioinformática si tiene ya conseguido un Master. Publicaciones recientes del grupo en este campo son:
• E. Capriotti & M. A. Marti-Renom “Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.” BMC Bioinformatics 11, 322 (2010).
• E. Capriotti & M. A. Marti-Renom, RNA structure alignment by a unit-vector approach. Bioinformatics 24, i112 (2008).
• E. Capriotti & M. A. Marti-Renom, Computational RNA structure prediction. Current Bioinformatics 3, 32 (2008).
Se valorará conocimientos de biología y, en concreto, conocimientos de biología estructural de RNA. Se requiere programación en C++ y Python.
Interesad@s contactar antes del 18/Feb/2011 enviando un e-mail a [email protected]. Especificar en el e-mail las razones para unirse a nuestro grupo así como un Cv detallado del candidato.
Marc A. Marti-RenomStructural Genomics UnitCentro de Investigación Príncipe Felipe46012 Valencia, EspañaTel. (+34) 963 289 [email protected]
We seek a BSc in Bio*, Physics, Mathematics, Computer Science or similar. Our group, located in the city of Valencia in Spain, offers competitive salaries and an excellent environment for scientific research.. To know more about our research group, follow this link: http://sgu.bioinfo.cipf.es.
The candidate will participate in the development and implementation of new methods for RNA structure prediction using the Integrative Modeling Platform. This project is supported by the Spanish Ministry on Science and Innovation. The initial contract will be for a a testing period that can be extended to a maximum of two years and a half. The candidate will also have the opportunity to pursue a PhD. To that end, a Master in Bioinformatics will be essential.
Recent publications of our group in this line of research are:
• E. Capriotti & M. A. Marti-Renom “Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.” BMC Bioinformatics 11, 322 (2010).
• E. Capriotti & M. A. Marti-Renom “RNA structure alignment by a unit-vector approach.” Bioinformatics 24, i112 (2008).
• E. Capriotti & M. A. Marti-Renom “Computational RNA structure prediction.” Current Bioinformatics 3, 32 (2008).
Knowledge of Biology and in particular RNA structural biology is desirable. Programming in C++ and Python is required.
Interested candidates should contact us before the 18/Feb/2011 by e-mail to [email protected]. The e-mail should contain your Cv as well as a cover letter indicating the reasons to join our group.
Marc A. Marti-RenomStructural Genomics UnitCentro de Investigación Príncipe Felipe46012 Valencia, EspañaTel. (+34) 963 289 [email protected]
Capriotti and Marti-Renom BMC Bioinformatics 2010, 11:322http://www.biomedcentral.com/1471-2105/11/322
Page 3 of 10
Figure 1 Accurate RNA structure alignments. (A) Staphylococcus phage group I ribozyme (1y0q PDB identifier, chain A) superimposed to a fragment a synthetic construct group I Intron (1u6b PDB identifier, chain B). (B) tRNA(Leu) of Pyrococcus horikoshii (1wz2 PDB identifier, chain C) superimposed to the tRNA(Met) of Acuifex aeolicus (2ct8 PDB identifier, chain C). (C) Superimposition of two synthetic constructs P4-P6 RNA ribozyme domain (1l8v and 2r8s PDB identifiers, chains A and R). (D) 23S ribosomal RNA of Haloarcula marismortui (3cce PDB identifier, chains 0) superimposed to the 23S ribosomal RNA of Thermus thermophilus (3d5b PDB identifier, chain A).
Staphylococcus phage group I ribozyme (1y0q:A)Synthetic I Intron fragment (1u6b:B)
Aligned nucleotides: 120RMSD: 1.8 ÅSequence Identity: 34.0 %Secondary Structure Identity: 52.1 %Structure Identity: 60.9 %Sequence -ln(p-value): 18.2Secondary structure -ln(p-value): 10.3Structure -ln(p-value): 15.6Mean -ln(p-value): 14.7
Synthetic P4-P6 RNA ribozyme (1l8v:A)Synthetic P4-P6 RNA ribozyme (2r8s:R)
Aligned nucleotides: 134RMSD: 1.8 ÅSequence Identity: 80.9 %Secondary Structure Identity: 81.0 %Structure Identity: 85.4 %Sequence -ln(p-value): 37.0Secondary structure -ln(p-value): 17.1Structure -ln(p-value): 19.4Mean -ln(p-value): 24.5
Pyrococcus horikoshii tRNA(Leu) (1wz2:C)Acuifex aeolicus tRNA(Met) (2ct8:C)
Aligned nucleotides: 65RMSD: 1.9 ÅSequence Identity: 56.8 %Secondary Structure Identity: 88.5 %Structure Identity: 87.8 %Sequence -ln(p-value): 10.2Secondary structure -ln(p-value): 5.2Structure -ln(p-value): 7.2Mean -ln(p-value): 7.5
A
DC
B
Haloarcula marismortui 23S RNA (3cce:0)Thermus thermophilus 23S RNA (3d5b:A)
Aligned nucleotides: 2,347RMSD: 1.7 ÅSequence Identity: 52.7 %Secondary Structure Identity: 75.7 %Structure Identity: 85.2 %Sequence -ln(p-value): 37.0Secondary structure -ln(p-value): 37.0Structure -ln(p-value): 37.0Mean -ln(p-value): 37.0