imported>GPbernet at 11:46, 5 July 2011

2011-07-05T11:46:06Z

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'''MATERIALS AND METHODS'''

'''Annotation and data mining'''

We used the set of scaffolds provided by the first assembling of the Pea aphid ''Acyrthosiphon pisum'' LSR1.AC.F1 strain genome to map transposable element (TE) features, as described in ([[literature:100813|IAGC 2010]]). Among the different mobile genetic elements (MGEs) characterized we identified 549 LTR retroelement-like features belonging or related to the ''Ty3/Gypsy'', ''Bel/Pao'' and ''Ty1/Copia'' families. The sequences were curated via BLASTx, tBLASTn and BLASTp ([[literature:85466|Altschul ''et al''. 1997]]) searches on the basis of their similarities to other LTR retroelements classified at GyDB ([[literature:100827|LLorens et al. 2011]]) and RepBase ([[literature:100828|Jurka ''et al''. 2005]]) by combining the version of Apollo ([[literature:100829|Lewis ''et al''. 2003]]) distributed by International Aphid Genomics Consortium (IAGC) and the GPRO (Gypsy Database Professional) software ([[literature:100830|Futami ''et al''. 2011]]) which implements a bioinformatic annotation pipeline.

'''Mobilomics Server design'''

The Mobilomics was programed as a PHP/JavaScript module completely integrated on the GyDB wiki system as a dynamic set of templates that queries a MySQL database which contains the complete set of mobilomes organized by organisms.

Mobilomics-acyrthosiphon pisum-Materials and Methods - Revision history

imported>GPbernet at 11:46, 5 July 2011