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? >>>> CCGIYCHEEPQREDSSI >>>> >r2 >>>> AVSHQEMNEGEQGPMREGSC >>>> ** >>>> human 10 PQREDS 15 + 8.13 >>>> r2 14 PMREGS 19 + 8.21 >>>> PMREDS >>>> Q G >>> CSGVYCHEEPQGEDSSV >>> >r2 >>> AVSHQEMNEGEQGPMREGSC >>> *** >>> mouse 7 HEE 9 + 6.26 >>> r2 4 HQE 6 + 6.03 >>> HEE >>> Q
 * Comparison of human to 5 random peptides
 * Human peptide comparison
 * Input
 * >human
 * Output
 * Score: 7.15938 Columns: 6 Sequences: 2
 * Mouse peptide comparison
 * Input
 * >mouse
 * Output
 * Score: 5.95133 Columns: 3 Sequences: 2

The score for the mouse peptide match was lower and the PQRE did not match with the PQGE.