Quick comparison of peptides 2-23-12
2015-01-13azim58 - Quick comparison of peptides 2-23-12
Shen wants to see how similar the mouse and human peptide sequences are.
All sequences
>mouse
CSGVYCHEEPQGEDSSV
>human
CCGIYCHEEPQREDSSI
>r1
TISKYVMVEPMRQHEEWGSC
>r2
AVSHQEMNEGEQGPMREGSC
>r3
RVGEMPMREYDISGGSGGSC
>r4
TAFYRTLTKHEVDPGIAGSC
>r5
WKPVPMRDFRTQPLMGDGSC
The main site of interest is the "PQRE" in the human. The mouse has a
"PQGE" instead.
R corresponds to arginine a polar positively charged amino acid
G corresponds to glycine a nonpolar neutral amino acid which is also the
simplest amino acid that exists
These are two very different amino acids.
What kind of scores will GLAM2 give?
- Comparison of human to 5 random peptides
- Human peptide comparison
- Input
@ >human
CCGIYCHEEPQREDSSI
>r2
AVSHQEMNEGEQGPMREGSC
- Output
@ Score: 7.15938 Columns: 6 Sequences: 2
**
human 10 PQREDS 15 + 8.13
r2 14 PMREGS 19 + 8.21
PMREDS
Q G
- Mouse peptide comparison
- >mouse
CSGVYCHEEPQGEDSSV
>r2
AVSHQEMNEGEQGPMREGSC
o Output
- Score: 5.95133 Columns: 3 Sequences: 2
***
mouse 7 HEE 9 + 6.26
r2 4 HQE 6 + 6.03
HEE
Q
The score for the mouse peptide match was lower and the PQRE did not
match with the PQGE.