[Baypiggies] upper case, lower case, and....?

[Nathan Pease]

do you have to change the entire peptide to lower-case? Are you changing it only to visually identify the peptide? why not surround it by characters that don't already have meaning (brackets maybe)?

If you have to user lower-case for the peptide you could also put some sort of escape char before the lower case 's' before converting the peptide, maybe a slash or a dash or something?

nate

On Apr 1, 2011, at 6:01 AM, Vikram K wrote:

> I have this protein sequence (each character represents an amino acid):
> 
> MAKFNTGSNPTEEAATSSRPFKVAGQSSPSGIQSRKNLFDNQGNASPPAGPSSMPKFGTTKPPLAAKPTYEEKPEKEP
> KPPFLKPTGGSPRFGTQPNSVSRDPEVKVGFLKPVSPKPTSLTKEDSKPVVLRPPGNKLHNLNQESDLKTPGPKPGPAP
> PVPENELKPGFSKVAGAKSKFMPAAQDTDSKPRFPRHTFGQKPSLSTEDSQEENTSKNVPVQKGSPVQLGAKSKGAPF
> KPPKEDPEDKDHGAPSSPFPGVVLKPAASRGSPGLSKNFEEKKEDRKTDLAKNIFLNKLNQEEPARFPKAPSKLTAGTPW
> GQSQEKEGDKNSATPKQKALPPLSVLGPPPPKPNRPPNVDLTRFRKADSANSATKSQTPYSTTSLPPPPPTHPASQPPLPASHP
> AHPPVPSLPPRNIKPPLDLKHPINDENQDGVMHSDGTGNLEEEQESEGETYEDIDSSKERDKKREKEEKKRLELERKEQKEREKK
> EQELKKKFKLTGPIQVIHHAKACCDVKGGKNELSFKQGEDIEIIRITDNPEGKWLGRTARGSYGYIKTTAVEIDYDSLKRKKNSLNAVP
> PRLVEDDQDVYDDVAEQDAPNSHGQSGSGGMFPPPPTDDEIYDGIEEEDDDDGSVPQVDEKTNAWSWGILKMLKGKDDRKKSIRE
> KPKVSESDNNEGSSLPSQHKQLDVGEEVYDDVDASDFPPPPAEMSQGMSVGRAKTEEKDPKKLKKQEKEEKDLRKKFKYDGEIRVL
> YSTKVASSLTSKKWGARDLQIKPGESLEVIQSTDDTKVLCRNEEGKYGYVLRSYLVDNDGEIYDDIADGCIYDND
> 
> I identified the presence of the following peptide sequence in this protein:
> TTAVEIDYDsLKR
> 
> The small s ('s') in the peptide sequence represents a phosphoyrlated serine (phospho serine) which is different from a normal serine which is represented by 
> the big s ('S').
> 
> Now i replace the occurence of the peptide in the protein with small case to identify where the peptide is occuring in the protein:
> 
> MAKFNTGSNPTEEAATSSRPFKVAGQSSPSGIQSRKNLFDNQGNASPPAGPSSMPKFGTTKPPLAAKPTYEEKPEKEPKPPFLKPT
> GGSPRFGTQPNSVSRDPEVKVGFLKPVSPKPTSLTKEDSKPVVLRPPGNKLHNLNQESDLKTPGPKPGPAPPVPENELKPGFSKVA
> GAKSKFMPAAQDTDSKPRFPRHTFGQKPSLSTEDSQEENTSKNVPVQKGSPVQLGAKSKGAPFKPPKEDPEDKDHGAPSSPFPGVVL
> KPAASRGSPGLSKNFEEKKEDRKTDLAKNIFLNKLNQEEPARFPKAPSKLTAGTPWGQSQEKEGDKNSATPKQKALPPLSVLGPPPPKP
> NRPPNVDLTRFRKADSANSATKSQTPYSTTSLPPPPPTHPASQPPLPASHPAHPPVPSLPPRNIKPPLDLKHPINDENQDGVMHSDGTGNL
> EEEQESEGETYEDIDSSKERDKKREKEEKKRLELERKEQKEREKKEQELKKKFKLTGPIQVIHHAKACCDVKGGKNELSFKQGEDIEIIRITDN
> PEGKWLGRTARGSYGYIKttaveidydslkrKKNSLNAVPPRLVEDDQDVYDDVAEQDAPNSHGQSGSGGMFPPPPTDDEIYDGIEEEDDDDGSV
> PQVDEKTNAWSWGILKMLKGKDDRKKSIREKPKVSESDNNEGSSLPSQHKQLDVGEEVYDDVDASDFPPPPAEMSQGMSVGRAKTEEKDP
> KKLKKQEKEEKDLRKKFKYDGEIRVLYSTKVASSLTSKKWGARDLQIKPGESLEVIQSTDDTKVLCRNEEGKYGYVLRSYLVDNDGEIYDDIADGCIYDND 
> 
> My problem is that i wish to distinguish the phospho serine character from the rest of the small case letters in the modified protein sequence shown above.
> Any suggestions? 
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