Quick comparison of peptides 2-23-12

2015-01-13

azim58 - 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
  o Input
    - >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.

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