Talk:BE.109:Bio-material engineering/Sequence analysis

Tuesday/Thursday Lab Sequence Data

team color	candidate number	sequence	relative strength	comments/notes
Green	A	XXWAPAXXXXXX	1/18 of pCT-CON	This sequence did not show significant binding ability, although because of the poor sequencing data, we can not make any definite conclusions on the cause of the poor gold binding ability.
Green	B	XXXXVGXXXXXX	3.5 of pCT-CON	This sequence has some gold binding ability, however unlike D, the sequence data obtained for this colony is quite poor. As a result, we can not make any definite conclusions on what lead to it's binding.
Green	C	XXXXXXXXSLFL	.83 of pCT-CON	This sequence did not show significant binding ability, although because of the poor sequencing data, we can not make any definite conclusions on the cause of the poor gold binding ability.
Green	D	LRXXTXGLSLCR	7.83 of pCT-CON	Colony D was the only one from which we got some sort of meaningful sequence data from. Luckily, it was also our strongest binder. The sequence data shows a prevalence of Yellow Aliphatic Groups (Leucine) and Green Hydroxyl Groups (Serine), which may be important for gold binding.
Purple	B	WRxxxACRCVxx	0.3 x pCT-CON	2 cysteines may be signficant
Purple	C	MYYVAASxSVLM	2 x pCT-CON	2 methionines and 2 serines may be significant
Purple	D	*LARPVA*xxIx	10 x pCT-CON	best binder. stop codons are TAG and TGA
Yellow	A	EXXXPIXXXXXX	1.89 of pCT-CON	We do not know very much about sequence A, but we hypothesize that it contains aromatic amino acids. Here is a color coded chart of our sequences:
Yellow	B	RXRLRVXXXXVR	0.413 of pCT-CON	This sequence is the weakest gold binder and also exhibits the most amount of basic amino acids, which indicates that basic amino acids may prevent gold binding. Sequence A shows no basic amino acids, and sequence D contains two basic amino acids which may be the reason that sequence A bonds gold more strongly than sequence D, despite its lack of aromatic amino acids.
Yellow	C	EGXXPXXXXXXX	0.55 of pCT-CON	We do not know very much about sequence C. One observation that we had about sequences B and C is that they contained no aromatic residues, but they did contain acidic amino acids. But there is still even a chance that C and A are identical.
Yellow	D	FWCQSRWXEILV	1.72 of pCT-CON	This sequence contains three aromatic residues, which is rare in the library, which is a significant feature. Also, the weakly binding sequences (B and C) do not show any aromatic residues, which indicates that aromatic residues may be responsible for gold binding.
Blue!	A	LCVIQAXXKSIV	relatively good	Binding: more colonies than pCT-CON, but much less than on pAu1. Sequence: This sequence contains lots of aliphatic residues, and one cysteine.
Blue!	B	XXXXXPXXXRXX	not good	Binding: As many colonies formed as pCT-CON. Sequence: We do not have enough sequence data to comment on this sequence.
Blue!	C	XXXXXXXXXXAX	good binder	Binding: More colonies than pCT-CON, but much less than on pAu1. Sequence: We do not have enough sequence data to comment on this sequence.
Blue!	D	LXXXXXXXGMGX	good binder	Binding: More colonies than pCT-CON, but much less than on pAu1. Sequence: We do not have enough sequence data to comment on this sequence (has at least two Glycines though!).
Pink	A	VAASRLVCCXXXL	6 x pCT-CON	2 cysteines right next to each other might mean that disulfide bonds cannot occur so sulfur available to bind to gold.
Pink	D	XXADKLLXHAPQ*	6 x pCT-CON	Histidine present which if we enrinched the species, histidine would probably be present in greater amounts :)

Wednesday/Friday Lab Sequence Data

team color	candidate number	sequence	relative strength	comments/notes

HAVE A GREAT SUMMER!!