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BBF RFC 56: “Part Flavors” For Peptide-Coding Parts

Research and Teaching Output of the MIT Community

Show simple item record Anderson, J. Chris 2010-10-11T14:23:17Z 2010-10-11T14:23:17Z 2010-10-11
dc.description.abstract “Part Flavors” are a means of describing the grammatical properties of parts. Specifically, this is introduced as a means of describing parts that encode peptides (CDS parts), but there may be value to extrapolating the concept to other types of parts. A CDS part flavor is intended to address the problem of how to precisely describe compositions of parts that differ by the presence of 5’ and 3’ spacers, presence or absence of start codons, stop codons, and ribosome binding sites, etc. The goal is to be able to describe these in such a way that grammar-based software tools (such as Genocad or Eugene) could register the grammatical equivalence of two parts. This facilitates automated design strategies in which an abstract device (such as promoter.rbs.CDS.terminator) can be instantiated to grammatically correct compositions (such as r0040.b0034.E0040.b0015). The concept is an extension of RFC 13 which proposes to describe CDS parts as “head,” “internal,” “special,” or “tail” domains. The difference is a little subtle, it has nothing to do with what the part encodes per se, but rather seeks to distinguish the translation-related properties of the encoded part and separate them into grammatically-equivalent categories, and in so doing allows for there being more “flavors” of part that can exist (and already do exist). I describe the concept here since we’ve been using this concept for the past 2 years or so, and there are already a number of parts whose descriptions are written with the flavor notations described herein in the Registry. This document serves as a guide to interpreting the codes. This may also be of value to others as a means of distinguishing their different types of parts. en_US
dc.language.iso en_US en_US
dc.relation.ispartofseries BBF RFC;56
dc.rights Attribution-No Derivative Works 3.0 United States en
dc.rights.uri en
dc.subject part en_US
dc.subject grammar en_US
dc.title BBF RFC 56: “Part Flavors” For Peptide-Coding Parts en_US
dc.type Technical Report en_US

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