2005-05-05

    Nueva plataforma de microarrays para Danio rerio

    En breve salgo para Gouda-Rotterdam-Kinderdijk, pero antes un poco de ciencia.

    Uno de los puntos de mi artículo es señalar la inutilidad de los recursos genómicos si se carece de una anotación de calidad. En el caso del pez cebra, aunque mejora. Por ejemplo, las tres plataformas de microarray disponibles hasta la fecha está basada en las ESTs disponibles, con sus anotaciones originales, algunas datando de 1998. Así, ninguna de ellas es completa, y por señalar un caso emblemático, el complemento de genes Hox no está entero en ninguna de ellas, y muchos de ellos están mal anotados. Haciendo esto extensible al resto del genoma, en realidad lo único de que sirven es para análisis exploratorio y con un fuerte componente de revisión manual de los datos.

    Afortunadamente el genoma está cada vez más cerca de estar completado, la mayoría de los genes ya han sido secuenciados y sólo queda mejorar el ensamblaje de los contigs. Nuestro grupo ha diseñado un conjunto de sondas basándonos en información genómica con los que completamos los recursos disponibles. Hasta la fecha.

    Agilent, mi empresa favorita en esto de microarrays, ha sacado una librería de 21495 sondas diseñadas de acuerdo con la secuencia del genoma y utilizando las anotaciones más recientes disponibles. Y además, permite la personalización al dejar al usuario añadir sus propias secuencias a la versión comercial. Una maravilla, oiga.

    A ver si convenzo a mis jefes de que aflojen la pasta...

Referencias (TrackBacks)

URL de trackback de esta historia http://evolucionarios.blogalia.com//trackbacks/29451

Comentarios

1
De: Ana Fecha: 2005-05-05 15:40

Dices que el ensamblaje del genoma de D. rerio esta por terminarse. A la ultima conferencia que fui yo se discutieron varios problemas que habian surgido con este proyecto. No he seguido los detalles en este ultimo anyo, pero quizas me podrias sacar de dudas. La secuenciacion del genoma se hizo con el metodo "shotgun" que es el utilizado hoy en dia y el ensambaje se hace utilizando los contings secuenciados como referencia. El problema en su dia fue que las especies elegidas para originar los contings y la(s) utilizadas para la secuenciacion del genoma eran distintas y el grado de polimorfismo entre estas hacia el ensamblaje muy dificil. Yo por lo menos en su dia encontre la utilizacion del ensamblaje realmente limitada y no muy fiable. Se ha resuelto este tema? Y teniendo esto en cuenta, afectaria al disenyo de la libreria de Agilent?

Food for thought....



2
De: Ana Fecha: 2005-05-05 15:54

Perdon, no quise decir especie sino "strains" (que en bacterias es cepa pero en organismos pluricelulares no se como se llama). Con tanta traduccion me armo un lio yo sola.



3
De: Anónima Fecha: 2005-05-05 22:33

Tenía curiosidad por ver información sobre microarrays en Agilent, pinché el link y no va. De todas formas tienen un buscador y es impresionante la cantidad de información que tienen y lo bien que se busca.



4
De: BioMaxi Fecha: 2005-05-06 08:59

http://www.chem.agilent.com/scripts/literaturepdf.asp?iwhid=40119

http://www.chem.agilent.com/temp/rad97966/00051952.pdf

Decidme si funcionan estos dos, y así cambio los enlaces en la historia.



5
De: BioMaxi Fecha: 2005-05-06 09:07

Ana, no sé en que línea se hizo el mapa genético, pero el shotgun es Tübingen. Los de Sanger nos explicaron (tenemos colaboración con ellos) que en cualquier caso el nivel de SNPs de una línea es mucho mayor que el de toda la especie humana, por ejemplo, y que los algoritmos se hacen la picha un lío, por decirlo en plata. Afortunadamente poco a poco va avanzando el proyecto de secuenciación de BAC clones, que al ser más grandes facilitan el ensamblado. De hecho, ya hay una nueva versión 'pre ENSEMBL' sin anotación, pero con la primera versión de este segundo tipo de secuenciación.

En cualquier caso, todos los genes que he buscado se han encontrado, el problema es que ligamientos incluso muy estrechos se pierden, las secuencias intergénicas, al estar menos conservadas, sufren más. Por eso usando los genes predichos puedes tener muy buena cobertura del genoma, ideal para microarrays, pero para estudios de genómica estructural o comparativa (predicción de secuencias ultraconservadas, etc) aún queda algo.



6
De: Anónima Fecha: 2005-05-06 10:55

La página del post y la segunda del comentario 4 dicen:

"This page isn't available or has been updated."

El primer link si que funciona.



7
De: ciencia Fecha: 2005-05-07 01:45

El software de agilent es sencillamente genial.



8
De: Asombr8-S Fecha: 2005-05-07 18:00

A raíz del debate para cuestionar la teoría de Darwin en los textos escolares de USA, sobre todo la idea de que el hombre, el mono y otros animales tienen antepasados comunes, he publicado un artículo en mi blog. Quería saber vuestra opinión de expertos, ya que soy un aficcionado, si estoy equivocado en algo me gustaría saberlo.

Saludos y gracias.



9
De: pedro Fecha: 2006-05-05 12:07

esta pagina es una puta mierda jodidos listos meteros con buestras putas madres



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De: Liliana Hoyos Fecha: 2009-04-20 14:25

Cuál es el mejor software para microarrays y porque?



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