Hi,
I was trying to find something like the prosite rules database that may be
include more conserved domains.
That is, I've got a bunch of short peptides and I want to determine if any of
them have functional
significance. I would imagine that function prediction servers may have such
database but probably
not in downloadable form. In particular, I took about 3000 short sequences that
have something to
do with cell cycle arrest ( eutilsnew is my own script but you get the idea),
eutilsnew -protein -v -out stuff '"cell cycle" arrest'
$progpath/file_parsing -fastas stuff stuff_fasta
I have a way to get the most frequently occuring short strings. In this case, I
got some interesting hits,
( and also found out that "M" occurs at the start quite often, adding some
confidence that the code is running
properly...)
$progpath/string_test -fastas stuff_fasta -status -conserved | grep [A-Z] |
sort -g -r -k 2 > cca_roots
$ head cca_roots
M 2321
PENL 565
L 545
FENL 461
YENL 458
F 456
W 455
WENL 454
MS 425
RSPS 396
In any case, I wanted to see if the regular expression [PFYW]ENL means anything.
First, I did get a control group,
( only got the first 1500 and used ctrl-c to "select" the first few),
eutilsnew -v -protein -out some_hydo "hydroxylase"
$ head hydro_roots
M 1418
GDAA 312
GAGL 308
DAAH 299
AGLL 283
GLLS 266
IGLA 263
PVAG 258
LLSS 253
AGQG 253
The prosite rule list that I have shows some "ENL" candidates explicitly( non
of which
include PWY or W as a leading acid ) and maybe more that
are more cryptic,
$ grep ENL /cygdrive/c/mydocs/scripts/cc/affx/prosite_rules
P.{2}[LIVMF]{2}[LIVMS].[GDN].{3}[DENL].{3}[LIVM].E.{4}[GNQKRH][LIVM][AP]>rule|216|PEPDTIDE
Prosite RIBOSOMAL_S2_2
K[LIVMF]DG[LIVMAS][SAG].{4}Y.{2}[GRD].[LF].{4}[ST]RG[DN]G.{2}G[DE][DENL]>rule|832|PEPDTIDE
Prosite DNA_LIGASE_N1
CC[SHYN].{0,1}[PRG][RPATV]C[ARMFTNHG].{0,4}[QWHDGENLFYVP][RIVYLGSDW]C>rule|1104
|PEPDTIDE Prosite ALPHA_CONOTOXIN
but that is all I have to go on. I did a quick look at NCBI CDART and related
pfam resources but
couldn't figure out how to download anything useful. I couldn't immediately
get blast to return
any hits on "ENL" and I'm not sure what all parameters I'd need to tweak to
search on short things.
Thanks.
Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
415-264-8477 (w)<- use this
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here. Thanks.
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