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Wednesday, April 19, 2006

pattern in 3A

sequence for 3A in fasta format

>1
NFMLNQPHSVSESPGKTVTISCTRSSGNIDSNYVQWYQQRPGSAPITVIYEDNQRPSGVPDRFAGSIDRSSNSASLTISGLKTEDEADYYCQSYDARNVVFGGGTRLTVLG
>2
ESVLTQPPSASGTPGQRVTISCTGSATDIGSNSVIWYQQVPGKAPKLLIYYNDLLPSGVSDRFSASKSGTSASLAISGLESEDEADYYCAAWNDSLDEPGFGGGTKLTVLGQPK
>3
NVLTQPPSVSGAPGQRVTISCTGSNSNIGAGFTVHWYQHLPGTAPKLLIFANTNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSARFGGGTRLTVLG
>4
ASVLTQPPSVSGAPGQRVTISCTGSSSNIGAGHNVKWYQQLPGTAPKLLIFHNNARFSVSKSGTSATLAITGLQAEDEADYYCQSYDRSLRVFGGGTKLTVLR
>5
TALTQPASVSGSPGQSITVSCTGVSSIVGSYNLVSWYQQHPGKAPKLLTYEVNKRPSGVSDRFSGSKSGNSASLTISGLQAEDEADYYCSSYDGSSTSVVFGGGTKLTVLG
>6
ELTQPPSVSVSPGQTARITCSANALPNQYAYWYQQKPGRAPVMVIYKDTQRPSGIPQRFSSSTSGTTVTLTISGVQAEDEADYYCQAWDNSASIFGGGTKLTV
>7
YELIQPSSASVTVGETVKITCSGDQLPKNFAYWFQQKSDKNILLLIYMDNKRPSGIPERFSGSTSGTTATLTISGAQPEDEAAYYCLSSYGDNNDLVFGSGTQLTVLRGPKSSPKVTVFPPSPEELRTNKATLVCLVNDFYPGSATVTWKANGATINDGVKTTKPSKQGQNYMTSSYLSLTADQWKSHNRVSCQVTHEGETVEKSLSPAECL
>8
TWGVSSPKNVQGLSGSCLLIPCIFSYPADVPVGITAIWYYDYSGKRQVVIHSGDPKLVDKRFRGRAELMGNMDHKVCNLLLKDLKPEDSGTYNFRFEISSNRWLDVKGTTVTVTT
>9
SNRKDYSLTMQSSVTVQEGMCVHVRCSFSYPVDSDTDSDPVHGYWFRAWKAPVATNNPAWAVQEETRDRFHLLGDPQTKNCTLSIRDARMSDAGRYFFRMEKGNIKWNYKYDQLSVNVTALT
>10
SKAQVLQSVAGQTLTVRCQYPPTGSLYEKKGWCKEASALVCIRLVTSSKPRTMAWTSRFTIWDDPDAGFFTVTMTDLREEDSGHYWCRIYRPSDNSVSKSVRFYLVVS
>11
GKDIQVIVNVPPSVRARQSTMNATANLSQSVTLACDADGFPEPTMTWTKDGEPIEQEDNEEKYSFNYDGSELIIKKVDKSDEAEYICIAENKAGEQDATIHLKVFAK
>12
MPVAPYWTSPEKMEKKLHAVPAAKTVKFKCPSSGTPQPTLRWLKNGKEFKPDHRIGGYKVRYATWSIIMDSVVPSDKGNYTCIVENEYGSINHTYQLDVVERSPHRPILQAGLPANKTVALGSNVEFMCKVYSDPQPHIQWLKHIEVNGSKIGPDNLPYVQILKTAGVNTTDKEMEVLHLRNVSFEDAGEYTCLAGNSIGLSHHSAWLTVL
>13
NKRAPYWTNTEKMEKRLHAVPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGNYTCVVENEYGSINHTYHLDVVERSPHRPILQAGLPANASDVEFVCKVYSDAQPHIQWIKHVPYLKVLKAAGVNTTDKEIEVLYIRNVTFEDAGEYTCLAGNSIGISFHSAWLTVL
>14
KRAPYWTNTEKEKRLHAVPAANTVKFRCPAGGNP#VALUE!T#VALUE!WLKNGKEFKQEHRIGGYKVRNQHWSLI#VALUE!SVVPSDKGNYTCVVENEYGSINHTYHLDVVERSPHRPILQAGLPANASTVVGGDVEFVCKVYSDAQPHIQWIKHVEKNGSKYGPDGLPYLKVLKHSGINSSNAEVLALFNVTEADAGEYICKVSNYIGQANQSAWLTVLP
>15
GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT





in Pratt
use parameter:
-PN 60 -PX 10 -FL 100 -FP 100

let it match about 12 sequences

you'll get this pattern:
L-X-[IL]-X(2)-[ALV]-X(2)-[AES]-D-[AE]-[AG]-[ADE]-Y-X-C-X-[ASV]

play with the parameters, you'll get others.

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