[BiO BB] peptide identification tools question
Mike Marchywka
marchywka at hotmail.com
Tue Apr 24 11:36:19 EDT 2007
Hi,
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
LGNVWRFPY and
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
384 LGNVWRFPY
377 YL
376 CY
357 SF
352 FI
350 DA
347 LGN
345 YG
339 VA
333 WNT
328 NGGGAFL
315 YP
315 IF
( note new address as of 10-06)
Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165r
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