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 :)
Red	A	PDGT*LXVXXXX	3.125 x pCT-CON	Very similar to Sequence D. Similar relative strength to D. Has a proline next to a aspartic acid (acidic AA).
Red	B	DXXHPEYGPHCK	14.375 x pCT-CON	Very similar to sequence C. Similar relative strength to C. Has proline next to glutamic acid (acidic AA). Also has a proline further down sequence.
Red	C	XXXHPEYGPPXK	9.5 x pCT-CON	Very similar to sequence B. Similar relative strength to B. Has proline next to glutamic acid, and 2 prolines further down sequence next to each other.
Red	D	PDGT*LYXXXLX	.5 x pCT-CON	Very similar to sequence A. Similar relative strength to A. Has Proline next to aspartic acid (AA). --- Commonality between all four library sequences is presence of proline next to acidic AA, as well as extra prolines further into sequence.

Wednesday/Friday Lab Sequence Data

team color	candidate number	sequence	relative strength	comments/notes
Green	A	FXXXXXXXXXNX	~same as pCT-CON	This sequence did not display significant gold binding ability, and due to the poor sequencing data we can not make any definite conclusions on the cause of the poor gold binding ability.
Green	B	CGXXGAXPPLXL	~same as pCT-CON	2 prolines and 1 cysteine may be significant
Green	C	APEGKLXTRARX	~same as pCT-CON	1 proline and 3 basic amino acids may be significant
Green	D	EXXXXXXXXFSX	~same as pCT-CON	This sequence did not display significant gold binding ability, and due to the poor sequencing data we can not make any definite conclusions on the cause of the poor gold binding ability.
Pink	A	CGXXGAXXPXCL	a little bit less strong than pAu1	We see aliphatic and sulfur-containing AA's, as well as a Glycine and a Proline - which are important in determining the shape and rotation of the peptide.
Pink	B	pAu1		We must have accidentaly contaminated our samples with pAu1.
Pink	C	XXXFFXXXXX*	a little less strong than pAu1	We see no pattern between our two samples besides X's - : (
Pink	D	pAu1		See B - contamination - eek!
purple	A	unknown	.3xpCT-CON	Our peptide sequence data could not be determined because of the large number of ambiguities in the sequence of the DNA. This may be due to difficuly sequencing the DNA because it was not cleaned. This was actually the worst gold-binder.
purple	B	unknown	.4xpCT-CON	This peptide sequence data also could not be determined because of the ambiguities. This was the second-worst binder.
purple	C	unknown	1.7xpCT-CON	This was the best gold-binder, but the peptide sequence could not be determined.
purple	D	unknown	.78xpCT-CON	This was the second-best gold binder and had the same problems with the sequence data.
Red	A		.27xpCT-CON	Much of our peptide data (50%) could not be determined because of the large number of ambiguities. This was the weakest gold-binder.
Red	B	see above	2.67xpCT-CON	This peptide was our second strongest binder. It contained many types of amino acids, all except amide and sulfur-containing.
Red	C	see above	2xpCT-CON	This was the third strongest binder, perhaps because its sequence was truncated by four amino acids.
Red	D	see above	3.53xpCT-CON	This was the strongest gold binder. There was only one ambiguity in the sequence. Two prolines were adjacent to each other, a consistent trend with other groups as well.
Blue	A-D		Library samples A-C were stronger than pCT-CON. Library D bound with about the same strength as pCT-CON	2 Cysteins in sample B and 2 Glutaminein sample D could effect binding
Gold	A	LXXXX XXXXX PX	triple	lots of Xs
Gold	B	LXLGX XXXXX PP	same	some Xs
Gold	C	GSQXV AXXRX YX	triple
Gold	D	GXTXX MAXXX DX	Five times

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HAVE A GREAT SUMMER!!