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The description of the implementation of the framework for Clive and UNIX using the Go programming language.
Google Web Fonts, were also used and the tool was built on Google's App Engine using the Go Programming language.
Built by Michael Hoisie in one weekend using the GO programming language and Redis, the app currently has over 90,000 users.
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To understand the function of the SOX2 binding genes, we performed a GO analysis using the GO miner program using evidence level 3 of molecular functions.
By using the GO Slimmer program under the three level 1 categories (cellular components, molecular functions and biological processes), the 2489 unigenes (Supplementary Table S5) were then classified into 23 of 24 subcategories (second level GO terms) in the category of biological process, 13 of 14 subcategories in cellular component and 12 of 16 subcategories in molecular function.
Functional annotation of the proteins was performed using the Blast2 GO program against the non-redundant protein database at NCBI [ 28].
Software, called kpath, implementing the path encoding and decoding method was written in the Go programming language, using a translation of the arithmetic coding functions of Moffat et al.
In what follows we refer to the host system as UNIX, but note that any other system supporting the Go programming language may be used instead.
To test the underlying assumption that missing genes may be implicated in particular biological pathways, we examined their functional annotation in the context of Gene Ontology (GO) using the program GO Tree Machine [ 31].
GO SLIM terms were obtained using the program GO SLIM Viewer [ 61].
Associations with Gene Ontology, GenMAPP [58] and PANTHER [59]pathways were obtained using MAPPFinder 2.0 [42], a part of the GenMAPP 2.1 [41] application package and further filtered and annotated using the program GO-Elite (http://www.genmapp.org/go_elite/go_elite.html).html
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