Loading presentation...

Present Remotely

Send the link below via email or IM

Copy

Present to your audience

Start remote presentation

  • Invited audience members will follow you as you navigate and present
  • People invited to a presentation do not need a Prezi account
  • This link expires 10 minutes after you close the presentation
  • A maximum of 30 users can follow your presentation
  • Learn more about this feature in our knowledge base article

Do you really want to delete this prezi?

Neither you, nor the coeditors you shared it with will be able to recover it again.

DeleteCancel

Make your likes visible on Facebook?

Connect your Facebook account to Prezi and let your likes appear on your timeline.
You can change this under Settings & Account at any time.

No, thanks

trimethylaminuria

bioinf
by

Carolina Magro

on 31 October 2012

Comments (0)

Please log in to add your comment.

Report abuse

Transcript of trimethylaminuria

Trimethilaminuria: FMO3 Bioinformática 2012/2013 Árvores Filogenéticas Neighbor Joining tree vs. Maximum Likelihood tree Nos dóis métodos utilizados os valores de bootstrap variam, como esperado;


As distâncias obtidas foram concordantes com a evolução das espécies;
O organismo mais próximo do Homem é o Pan troglodytes (ingroup).
O mais distante do Homem é o Gallus gallus (outgroup)

Ingroup e outgroup previstos confirmaram-se, as espécies de outgroup são Gallus gallus e Sarcophilus harrisii. Conclusões Módulo 1 O Gene Ana Margarida Coelho
Ana Daniela Alves
Bruno Marques
Carolina Magro
Mykola Rasko Organismos Similares Pesquisa FMO3 flavin containing monooxygenase 3
[ Homo sapiens ] Sequência nucleótidos Homo sapiens flavin containing monooxygenase 3 (FMO3), transcript variant 1, mRNA

NM_006894 Desordem genética associada:
Síndrome do cheiro de peixe Alinhamento
das Sequências Similares http://www.ncbi.nlm.nih.gov/nuccore/NM_006894.5 Gene http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=2328 Dimethylaniline monooxygenase [N-oxide-forming] 3 [Homo sapiens] Outgroup: galo e diabo da tasmãnia Ingroup : todos os outros Caracteristicas: Transtorno metabólico;

Trimetilamina acumulada no organismo



Odor corporal semelhante ao
cheiro de peixe;

Presente desde o nascimento; Bos taurus Canis familiaris Macaca mulatta Mus musculus Oryctolagus cuniculus Pan troglodytes Rattus Norvegicus Sarcophilus harrisii Gallus gallus Diagnóstico: Medição da percentagem de trimetilamina presente na urina. Prevenir o odor: Evitar alimentos que contenham trimetilamina;
Uso de sabões ácidos; Neighbour Joining Blastn Uniprot Clustalw Sequência
de aminoácidos Determinação do d (modelo Poisson) d<1, logo os dados podem ser utilizados para fazer árvores NJ Métodos utilizados Neighbour Joining:
Converte as sequências alinhadas numa matriz de distâncias de diferenças par a par entre as sequências.

Maximum Likelyhood:
Usa o alinhamento múltiplo directamente e compara os caracteres em cada coluna do alinhamento. Cromossoma 1;
Braço q;
Localização 24.3; Figure. Molecular Phylogenetic anaylsis by Maximum Likelihood method

The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [1]. The tree with the highest log likelihood (-4544.8139) is shown. Initial tree(s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using a JTT model. The analysis involved 10 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 528 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [2].

1. Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.
2. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., and Kumar S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739. Cladograma com distâncias Bootstrap Cladograma com distâncias Figure. Molecular Phylogenetic anaylsis by Maximum Likelihood method

The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [1]. The tree with the highest log likelihood (-4544.8139) is shown. The percentage of trees in which the associated taxa clustered together is shown below the branches. Initial tree(s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using a JTT model. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site (below the branches). The analysis involved 10 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 528 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [2].

1. Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.
2. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., and Kumar S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739. 500 ciclos 500 ciclos Figure. Evolutionary relationships of taxa
The evolutionary history was inferred using the Neighbor-Joining method [1]. The optimal tree with the sum of branch length = 1.18083124 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown below the branches [2]. (below the branches). The evolutionary distances were computed using the JTT matrix-based method [3] and are in the units of the number of amino acid substitutions per site. The analysis involved 10 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 528 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [4].

1. Saitou N. and Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
2. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
3. Zuckerkandl E. and Pauling L. (1965). Evolutionary divergence and convergence in proteins. Edited in Evolving Genes and Proteins by V. Bryson and H.J. Vogel, pp. 97-166. Academic Press, New York.
4. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., and Kumar S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739. Nós Externos: 10
Nós internos: 8 Nós Externos: 10
Nós internos: 8 Figure. Evolutionary relationships of taxa
The evolutionary history was inferred using the Neighbor-Joining method [1]. The optimal tree with the sum of branch length = 1.18083124 is shown. The tree is drawn to scale, with branch lengths (below the branches) in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the JTT matrix-based method [2] and are in the units of the number of amino acid substitutions per site. The analysis involved 10 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 528 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [3].

1. Saitou N. and Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
2. Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.
3. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., and Kumar S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739. Jones-Taylor-Thornton (JTT) model Maximum Likelyhood Bootstrap Pesquisa de artigos Web of Knowlegde
Pub Med Wise, P. M., J. Eades, S. Tjoa, P. V. Fennessey and G. Preti (2011). Individuals Reporting Idiopathic Malodor Production: Demographics and Incidence of Trimethylaminuria. AMERICAN JOURNAL OF MEDICINE, ELSEVIER SCIENCE INC, 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA. 124: 1058-1063.

Christodoulou, J. (2012). "Trimethylaminuria: An under-recognised and socially debilitating metabolic disorder". JOURNAL OF PAEDIATRICS AND CHILD HEALTH. 48: E153-E155.

Phillips IR, S. E. (2007). Trimethylaminuria.

Shephard, E. A., E. P. Treacy and I. R. Phillips (2012). Clinical utility gene card for: trimethylaminuria. Journal Article; Research Support, Non-U.S. Gov't. 20 Formatação no EndNoteWEB, em CSE Style Manual C-S Neighbour Joining Tree Maximum likelihood Tree Jones-Taylor-Thornton (JTT) model Distâncias em relação a
Homo sapiens Homo Sapiens
Full transcript