Talk:20.109(S07): Bio-material engineering/Sequence analysis

Tuesday/Thursday Lab Sequence Data

team color	candidate number	sequence	relative strength	comments/notes
Green	A	XXXXXYXXXXXXXXXSGGXXSGGGXSAXQGXXXXGXXXXXXXXRXXXXXAXPXXXXXXXTXAYFXXXLXIXXXXXXTXXXXXXXXXSXXVFXDNS STIEGXXPXXXPXXALXXXXXXXXXXXXXXXXXXAXXXDXXXGXXXXXXXGXXXXXXXXXXAXXXXXTKXXXXXXXXXXXXXXXXXXXXXXXXXXX	as strong as pAu1	too many unknown codons to analyze
Green	D	XXXXXYALQASGGGGSGGGGSGGGGSASQGGGGSGTRMRDAWXLMKGYLARPVAXXRIRTKAYF*RGLVIARDLITTXXM*XXXLXXXXVFXDN XSXXXXXXXXKTXXTXXXY*VXXXXNSLXXXXXGXXXXR*XXXRRXFXXW*GDLXXXXXQFLXXXXXXNXXXXXTXXXLXLX*XXMXXNSIXYXXX	as strong as pAu1	seems as if the first stop codon may have mutated into a tyrosine, thus giving a longer gold-binding sequence
Purple	D	SGGGG SGGGG SGGGA SEIVL TQSPA LLSLS PGXRA TLSCR TSQSI SSTYL AWYQQ KPGQA PRLLI YGTSG RXTGI PYRFQ WXGSG XDFTX TISRL EPEDF AVXYC QQXAT SPRLL XGDQG GDQIR NSRTK AYF*R RLXXX XAASR SDTXC XC	weaker than pAU1	a few of the amino acids are conserved although the order is not. our sequence is longer than that of pAU1
Yellow	B	YALQA SGGGG SGGGG SGGGG SASQG GGXXX XXLXR XCXXL XXYXA RPVAX XRIRT KAYF*	weaker than pAu1	most of amino acids in variable region are uncertain
Yellow	D	YALQA SGGGG SGGGG SGGGG SASQG GGGXX LXLPT XCTXX GXXLA RXVAX XRIRT KAYF*	weaker than pAu1	sequence also fairly uncertain; no conserved amino acids observed, however, through trend of hydrophobic residues maintained
Blue	C	YALQA SGGGG SGGGG SGGGG SASQG GGGSG RMXD* TAXSN YF*LX RPV AXXRI RTKAY F*RGL VIARD LITTX XM*	weaker than pAu1	sequence was uncertain. There were no conserved amino acids. The sequence also has closely spaced stop codons compared to pAu1
Blue	D	YALQA SGGGG SGGGG SGGGX SASQG GGGSX XRGXR RXXEX GS*LX RPVAX XRIRT KAYF* RGLVI ARDLI TTXXM*	weaker than pAu1, but stronger than candidate C.	There are some conserved amino acids with pAu1. This might account for it being a better gold binder than candidate C.
sequence is very uncertain.	Pink	A	YAXQA SGGGG SGGGG SGGGG SASQG GGGSG SRXXX SXLYH FLXLA XPVAX XRIRT KAYF* RGLVI XXDLI TXXXM*	weaker binder than pAU1	presence of many uncertain amino acids
Pink	C	YALQA SGGGG SGGGG SGGGG SASQG GGGSG GRWIR CWQXX PXXLA RPVAX XRIRT KAYF*	weaker binder than pAU1	presence of many uncertain amino acids. Compared to candidate A, more amino acids match up with pAu1, better gold binder than candidate A.
Red	D	YALQA SGGGG SGGGG SGGGG SASQG GGGSG ERXLA CXKKF EWYLX RPVAX XRIRT KAYF	not really a gold binder (less colonies than pCT-CON)	Colony C sequencing failed, two glutamates in variable region

Wednesday/Friday Lab Sequence Data

team color	candidate number	sequence	relative strength	comments/notes
General	pCTCON	XXXXYALQASGGGGSGGGGSGGGGSASCGGGGTSKISHFLKMESLNFIRAHTPYINIYNC EPANPSEKNSPSTQYCYSIQSSQVDCGGGSEQKLISEEDLX*LEI**QXCXCNKIXFVQX TYCVFMGLPLLVVEG*EPQLLTNVTDL*YSKTPCIAFPLAKIVVVDKEYGVDSKVGEGIC SHIVVSSCAKTEAITENIEKQRSNCILIEXX*SRIXSXIXFX
General	pAu1	XXXXXXXXSXXXXXXXSRXXXXRXXXXCXXGTXXAXKXXTXEALXDXLTHLXHLXXXCLW QXXCL*XXXXXXIERXXXXXXXILHXXXXXXXXXSXXXXXXXXXXXXXXXXPXXXXSXTP GXXXXXXCXXXGX		failed sequencing
Green	B	XXXXYALQASGGGGSGGGGSGGGGSASQGGGGSGLFMQLLWAHLGC*LARPVAWGRIRTK AYF*RGLVIXRDLITTXXM*QNXLCSXXXCXVXXXXLLVVEG*EPQLLTNVTDL*YSKTP CIAFPLAKIXVVDKEYGVXSKVGEGICSHIVVSSCAKTEAITENIEKQRSNCILIENV*S XIXSFITFX
Green	C	XXXXXYALQASGGGGSGGGGSGGGGSASQXXXXXXXXTXXXXXXXXXXLXXXXXXXXWXX XXXXXXXXXXXEXXXXXXXXXXXXLXXXRXXXXXXXX*PSTXTXXXTSSPCX*TL*LPXT XLCITVQLXGTSXSIAXTGXXXPWXLSPXEF*DPVXXXXAVXXXXXXVXKLX*XSLRPFC LCLXGKXXPSPAGPVXXLAAPT*XXTSXNLXRLPXSXXXXXPAXXLASXXGXXXXXLGXT SLSPSXTXT*RFCXXXLXAXCXLTXXFWXXXXVEIKSXIXEQNXXLXXXXXXRXXXXXX* XXXX*XXXFXX
Purple
Yellow
Blue
Pink	7	XXXXYALQA SGGGG SGGGX SGGGX XAXXX GGGXG PRXXX XXXXX XXXXX XXXXX XXXXX XXXXX XXXXX XNXXX XXXMX XXXXX SXTXC VFMGL PLLVV EG*EP QLLTN VTDL* YSKTPC IAFPLAKIVVVDKEYGVDSKVGEGICSHIVVSSCAKTEAITENIEKQRSNCILIENV*SR IRSFITF	Approximately 3% of pAU1 binding
Pink	8	XXXYALQA SGGGG SGGGG SGGGG SASQG GGGSG TGPVR PKGXX KDXLA RPVXW GRIRTKA YF*RXXVXXXXLITTXXM*QNXLCSXXXXXXLWXCLC*LLRGENRNY*QTLLICNIQKLL ALPSRWPK**SLTKSTASILKLVRGFARI*LSVPVLKLKQ*QKILKNSEVTAS*LKMYEV EFDLLLHLX	Approximately 5% of pAU1 Binding
Red	sample b	YALQASGGGGSGGGGSGGGGSASQGGGXXX HAQPWGXXXXXX XLXXXXXXGXIXTKXYF*XGLVIXRDXITXXXM*XNXLCSXXXXXXXGXAFASC*GVRTAITDKRY*FVIFKNSLHCLPVGQNSSR*QRVRRRF*SW*GDLLAYSCQFLC*N*SNNRKY*KTAK*LHLN*KCMKXNSIFYYI*X	not too strong of a gold binder. only showed two more colonies over the PCT-CON. 8 compared to 6	sequencing obviously failed in the worst possible area. Our library potentially formed some sort of secondary structure obstructing the sequencing.
Red	sample c	YALQASGGGGSGGGGSGGGGSASQXGGGTX XXHGXXXXXXXL XLXXPVXXGXIXTKXYF*XGLVIXRDXXTTXXM*XXXLCSXXXXXGXGXAFASC*GVRTAITDKRY*FVIFKNSLHCLPVGQNSSR*QRVRRXF*SW*GDLLAYSCQFLC*N*SNNRKY*KTAK*LHLN*KCMKXNSIFYYI*X	moderately strong. 25 compared to the 6 on PCT-CON.	sequence failed in the library again....poor.

HAVE A GREAT SUMMER!!