Request "fingerprint contig", to go with FPCmap (SO:0001250)

[srynobio]

An FPCmap (SO:0001250) is often composed of several fingerprinted contigs (FPC). Currently there is no term for FPC. More info: The individual contigs are composed of several BACs (SO:0000153). The FPC map is the result of analysis of restriction site (?!) markers (SO:0001645), namely RFLP fragment (SO:0000193) markers (?!)... Can you also add a term for 'restriction site' and 'restriction site marker'? Sorry for overloading one request. Cheers, Dan

[srynobio]

Response from @keilbeck

Hi Dan OK, restriction site is the place where the enzyme cuts. WOuld you be happy with that being a synonym for the existing term restriction enzyme cleavage junction? restriction site marker - this is the sequence that is recognized by the enzyme? This terms exists already: restriction_enzyme_recognition_site. Would you be happy with a synonym? FPC is a contig? definition: contig composed of cloned sequence ordered by RFLP fragments Let me know if any of this works for you and changes you want to make. --KAren

[srynobio]

Response from Dan Bolser

Hi Karen, Yup "restriction enzyme cleavage junction" == "restriction site". A "restriction site marker" is a bit more complex, so I'm tempted to drop that request for now. Technically, its an "RFLP marker", i.e. an "RFLP fragment" used as a marker. Now I think about it, FPC is a bit tricky... actually FPC was originally derived from "FingerPrinted Contigs" named by the software called package called 'FPC'. Here is how they describe the software: "FPC takes as input a set of clones and their restriction fragments (called Bands) and assembles the clones into contigs" See:

• http://www.agcol.arizona.edu/software/fpc/
• http://www.agcol.arizona.edu/software/fpc/summary.html However, on the web and in the literature, the term 'FPC contig' has become used to name the resulting 'contigs'. It is important to note that this is an overloading of the term 'contig', because they don't mean sequence contigs, they mean 'BAC contigs' or 'physical contigs'... I'm not browsing the ontology just now, but I wonder if similar terms already exist, providing a clear precedent for creating a term 'FPC Contig' or similar... Your definition of 'FPC' is accurate. Hopefully the above answers your question "FPC is a contig?"? Thanks for taking the time to work on this. Dan.

[srynobio]

Response from @keilbeck

OK, FPC seems like it probably falls into the category of fragment assembly. Does this seem right to you? --K