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Select non-redundant sequences from:
Curagen
Ensembl/Human
FANTOM
GenenGenes
Geneseq
Incyte
MGC/Human
MGC/Mouse
Proteome
RefSeq
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
which meet these restrictions:
species is
Mouse (Mus musculus)
Rat (Rattus norvegicus)
Black rat (Rattus rattus)
Fruit fly (Drosophila melanogaster)
Zebrafish (Danio rerio)
Human (Homo sapiens)
Dog (Canis familiaris)
Cat (Felis silvestris catus)
NOTE: selecting species filtering will eliminate sequences whose species is not explicity denoted
fewer than
7d
14d
30d
60d
90d
180d
365d
old
length is between
and
AA
have signal sequence
and align
by HMM/Pfam
with eval <=
1e-40
1e-30
1e-20
1e-10
1
5
10
by PSI-BLAST/Structure Based Profiles
with eval <=
1e-40
1e-30
1e-20
1e-10
1
5
10
by Prospect Profile-Profile/Threading
with svm >=
13
12
11
10
9
8
7
6
5
using parameter set
1
to Genentech-curated sets of
ITxM to merge (set -1)
prospect_scop20 (set -1000)
E3 Ligase Domains (set -500)
TNF knowns (set 1)
Prospect2 FSSP (set 10)
ITxM (set 11)
PDZ (set 12)
Ig domains (set 13)
FnIII domains (set 14)
Kinases (set 15)
EGF domains (set 16)
POZ (set 17)
AAA-ATPase domains (set 18)
Bcl-2 domains (set 19)
TNF relatives (set 2)
Prospect3 FSSP (set 20)
Death Associated Domains (set 21)
TRIM helicase (set 23)
Helicases (set 25)
Pfam_fs 21.0 (set 26)
Pfam_ls 21.0 (set 27)
Prosite 20.15 (set 28)
Prosite 20.16 (set 29)
TNF superfamily (set 3)
Pfam_fs 22.0 (set 30)
Pfam_ls 22.0 (set 31)
Death Domains (set 5)
Cytokines - short (set 6)
Cytokines - long (set 7)
Cytokines - IL-10-like (set 8)
Cytokines - All (set 9)
models
EXCEPT sequences:
in set
Human (set 1)
Mouse (set 2)
Rat (set 3)
Zebrafish (set 4)
S. aureus (set 5)
archea (set 11)
bacteria (set 12)
eukaryota (set 13)
viridae (set 14)
initM (set 40)
bogus AA (set 45)
no run (set 49)
uniA (set 50)
uniB (set 51)
uniC (set 52)
runA (set 60)
runB (set 61)
runC (set 62)
runGGa (set 69)
uniblast (set 70)
patented (set 100)
patented 99% (set 101)
patented 98% (set 102)
patented 95% (set 105)
public (set 150)
NCBI Human (set 250)
SCOP - Fold Reps (set 500)
SPDI Published Sequences (set 900)
TNF ligand knowns (set 1000)
TNF knowns - human (set 1001)
TNF-like (set 1002)
TNF - human (set 1003)
TNFR (set 1010)
TNFR human (set 1011)
Death SF (set 1020)
DEATH (set 1021)
DED (set 1022)
CARD (set 1023)
Pyrin (set 1024)
Cytokine Curated (set 1030)
ITIM - GenenGenes knowns (set 1040)
ITIM - GenenGenes knowns and pcluster siblings (set 1041)
ITIM - Staub predicted (set 1042)
ITIM - Staub knowns (set 1043)
ITIM - Staub knowns & pcluster siblings (set 1044)
ITIM - hits (set 1045)
ITIM - hits & pcluster siblings (set 1046)
ITIM - Candidates (set 1047)
Kinases (set 1050)
Kinases - human (set 1051)
Bcl-2 knowns zebrafish (set 1060)
Bcl-2 knowns zebrafish Uniprot (set 1061)
Bcl-2 knowns zebrafish Refseq (set 1062)
Bcl-2 knowns zebrafish Ensembl (set 1063)
Bcl-2 knowns zebrafish Manual (set 1064)
Bcl-2 Family (set 1070)
RabGAPs Human (set 1080)
Rabs Human (set 1090)
Tough Nuts (set 5000)
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