[BiO BB] peptide identification tools question

Mike Marchywka marchywka at hotmail.com
Tue Apr 24 11:36:19 EDT 2007

I was looking into various issues surrounding 5HT. There seems to be  a lot 
confusion on
its role in depression and valvular heart disease among other things. I did 
a blast search on
SERT and then tried to make a frequency table of peptide hits using a simple 
text processing
script. While line breaks and other artifacts are surely messing up the 
details, I did find a couple
of interesting peptides I wanted to investigate. Just out of curiousity, 
what tools would I use
to investigate the longer more frequent peptides? I ran a blast search on 
tried to use the conserved domain search but the blast search didn't return 
anything surprising
and I didn't find anything related in conserved domain results but I wasn't 
sure I knew
how to use the output. Are these peptides well known or just likely 
artifacts and how
would I tell?  Thanks.
$ cat sert_peptides |more
816 PY
766 LG
502 LPW
495 VW
482 LL
464 FF
462 AV
437 GG
410 YY
395 TS
377 YL
376 CY
357 SF
352 FI
350 DA
347 LGN
345 YG
339 VA
333 WNT
315 YP
315 IF

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Mike Marchywka
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