./progs/mast $memeOutFname -d $fname -bfile $bgFname -nostatus -stdout -text -brief -ev 99999 -mev 99999 -mt 0.99 -seqp -remcorr
progs/mast

David J Reiss, Institute for Systems Biology
cMonkey integrated biclustering algorithm for learning co-regulated gene groups
RCurl, multicore, igraph, RSVGTipsDevice, fUtilities, hwriter

./progs/meme $fname -bfile $bgFname -psp $pspFname -time 600 -dna -revcomp -maxsize 9999999 -nmotifs %1$d -evt 1e9 -minw 6 -maxw 24 -mod zoops -nostatus -text -cons $compute -pal=non
progs/meme

-time 600 -dna -revcomp -maxsize 9999999 -nmotifs %1$d -evt 1e9 -minw %2$d -maxw %3$d -mod zoops

java -Xmx1000M -Xshare:off -jar SPACER.jar -b %s -o %s %s
java -Xmx1000M -Xshare:off -jar SPACER.jar -l %s -o %s %s

java -Xmx1000M -Xshare:off -jar SPACER.jar -b %s -o %s %s
java -Xmx1000M -Xshare:off -jar SPACER.jar -l %s -o %s %s

2-hydroxyglutaryl-CoA dehydratase subunit A-like protein
2-hydroxyglutaryl-CoA dehydratase subunit D-like protein
2-oxoacid ferredoxin oxidoreductase subunit beta
2-oxoglutarate ferredoxin oxidoreductase, delta (ferredoxin) subunit
2-oxoglutarate ferredoxin oxidoreductase subunit alpha
2-oxoglutarate ferredoxin oxidoreductase subunit beta
2-oxoglutarate ferredoxin oxidoreductase subunit gamma
3-dehydroquinate dehydratase (Type I DHQase)
ABC-type amino acid transport/signal transduction systems periplasmic component-related
ABC-type Iron(III)-binding periplasmic protein precursor
ABC-type iron(III) transport system, ATP binding protein
ABC-type iron(III) transport system, periplasmic binding protein
ABC-type iron(III) transport system, permease component
acetolactate synthase 3 regulatory subunit
acetyl-CoA decarbonylase/synthase complex subunit alpha
acetyl-CoA decarbonylase/synthase complex subunit beta
acetyl-CoA decarbonylase/synthase complex subunit delta
acetyl-CoA decarbonylase/synthase complex subunit epsilon
acetyl-CoA decarbonylase/synthase complex subunit gamma
AIR synthase related protein domain protein
amino acid ABC transporter ATP-binding protein
amino acid ABC transporter periplasmic protein
amino acid ABC transporter substrate-binding protein
amino acid ABC-type transporter related protein
aminotransferase (subgroup I) aromatic aminotransferase
aminotransferase (subgroup II) adenosylmethionine-8-amino-7-oxononanoate aminotransferase
anaerobic ribonucleoside-triphosphate reductase activating protein
ATPase, P-type (transporting), HAD superfamily, subfamily IC
ATP binding putative nickel incorporation protein
basic helix-loop-helix dimerization domain-containing protein
bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein
bifunctional short chain isoprenyl diphosphate synthase
binding-protein dependent transport system inner membrane protein
binding-protein-dependent transport systems inner membrane component
blue (type1) copper domain-containing protein
branched chain amino acid ABC transporter
carbamoyl phosphate synthase small subunit
carbohydrate kinase, YjeF related protein
cation diffusion facilitator family transporter
CheA signal transduction histidine kinase
class II aldolase/adducin family protein
cobalamin (vitamin B12) biosynthesis CbiG protein
cobalt ABC transporter inner membrane protein
cobyrinic acid a,c-diamide synthase:cobyrinic acid a,c-diamide synthase CbiA
coenzyme B12-binding:cobalamin-dependent methionine synthase, B12-binding
coenzyme F420 hydrogenase/dehydrogenase beta subunit domain protein
coenzyme F420-non-reducing hydrogenase subunit alpha
coenzyme F420-non-reducing hydrogenase subunit beta
coenzyme F420-non-reducing hydrogenase subunit delta
coenzyme F420-non-reducing hydrogenase subunit gamma
coenzyme F420-reducing hydrogenase delta subunit
coenzyme F420-reducing hydrogenase subunit alpha
coenzyme F420-reducing hydrogenase subunit beta
coenzyme F420-reducing hydrogenase subunit delta
coenzyme F420-reducing hydrogenase subunit gamma
cytidine/deoxycytidylate deaminase, zinc-binding region related protein
dihydroorotate dehydrogenase electron transfer subunit
DNA-directed RNA polymerase related protein
DNA-directed RNA polymerase subunit beta''
DNA repair and recombination protein RadA
DNA repair and recombination protein RadB
elongation factor Tu domain-containing protein
energy conserving hydrogenase A integral membrane subunit
energy conserving hydrogenase A large subunit
energy conserving hydrogenase A small subunit
energy conserving hydrogenase B integral membrane subunit
energy conserving hydrogenase B large subunit
energy conserving hydrogenase B small subunit
Fe-S type hydro-lyase tartrate/fumarate beta region
formate dehydrogenase family accessory protein FdhD
formylmethanofuran dehydrogenase subunit E related protein
glutamate synthase; large subunit; subunit 1
glutamate synthase; large subunit; subunit 2
glutamate synthase; large subunit; subunit 3
H/ACA RNA-protein complex component Cbf5p
H/ACA RNA-protein complex component Gar1
H/ACA RNA-protein complex component Nop10p
HAD superfamily (subfamily IA) hydrolase
H+-transporting two-sector ATPase, A subunit
hydrogenase nickel insertion protein HypA
hydrogen uptake protein:hydrogenase maturation protease HycI
hydroxymethylglutaryl-coenzyme A reductase:3-hydroxy-3-methylglutaryl coenzyme A reductase
imidazole glycerol phosphate synthase subunit HisF
imidazole glycerol phosphate synthase subunit HisH
indolepyruvate oxidoreductase subunit alpha 1
indolepyruvate oxidoreductase subunit alpha 2
K+-dependent Na+/Ca+ exchanger related-protein:Sodium/calcium exchanger membrane region
L-lysine/ homoserine-homoserine lactone exporter family protein
low molecular weight phosphotyrosine protein phosphatase
methanol dehydrogenase regulatory protein related protein
methyl coenzyme M reductase, component A2
methyl-coenzyme M reductase I, alpha subunit
methyl-coenzyme M reductase I, beta subunit
methyl-coenzyme M reductase I, gamma subunit
methyl coenzyme M reductase I, protein C
methyl-coenzyme M reductase I, protein D
microsomal signal peptidase 21 KD subunit
molybdate ABC transporter periplasmic substrate-binding protein
molybdenum ABC transporter ATP-binding protein
molybdenum ABC transporter periplasmic molybdate-binding protein
molybdenum ABC transporter, periplasmic molybdenum-binding protein
molybdenum ABC transporter, permease protein
molybdenum ABC transporter solute-binding protein
molybdenum cofactor biosynthesis protein A
molybdenum cofactor biosynthesis protein MoeA
molybdenum containing formylmethanofuran dehydrogenase, subunit B
molybdenum containing formylmethanofuran dehydrogenase subunit C
molybdenum containing formylmethanofuran dehydrogenase, subunit E
multiple resistance and pH regulation protein F
N-6 adenine-specific DNA methylase:N6 adenine-specific DNA methyltransferase, D12 class
(NiFe) hydrogenase maturation protein HypF
nitrogenase MoFe cofactor biosynthesis protein NifE
non-canonical purine NTP pyrophosphatase, rdgB/HAM1 family
nucleoside triphosphate: 5'-deoxyadenosylcobinamide phosphate nucleotidyltransferase
OB-fold nucleic acid binding domain-containing protein
oxidoreductase family protein member subunit alpha
peptidyl-prolyl cis-trans isomerase, cyclophilin type
phosphate ABC transporter inner membrane protein
polyferredoxin, associated with F420-non-reducing hydrogenase
putative iron transport system substrate-binding protein, C-term half
putative iron transport system substrate-binding protein, N-term half
putative molybdenum cofactor biosynthesis protein C
putative molybdopterin-guanine dinucleotide biosynthesis protein A
putative monovalent cation/H+ antiporter subunit B
putative monovalent cation/H+ antiporter subunit C
putative monovalent cation/H+ antiporter subunit E
putative monovalent cation/H+ antiporter subunit G
putative signal transduction protein with CBS domains
putative signal-transduction protein with CBS domains
putative transcriptional regulator, GntR family
putative transmembrane subunit of a hydrogenase
pyruvate ferredoxin oxidoreductase subunit beta
pyruvate ferredoxin oxidoreductase subunit gamma
pyruvate oxidoreductase (synthase) subunit alpha
pyruvate oxidoreductase (synthase) subunit delta
response regulator receiver modulated CheB methylesterase
ribosomal protein S6 modification enzyme (glutaminyl transferase) related
RNA 2'-O-methyl modification protein (NOP5/NOP56)
RNA methyltransferase, TrmH family, group 1
SbcD/Mre11 family DNA repair exonuclease
signal recognition particle-docking protein FtsY
Signal recognition particle protein SRP19
signal recognition particle protein Srp54
small nuclear ribonucleoprotein (Sm protein)
SSS sodium solute transporter superfamily
stress responsive alpha-beta barrel domain protein
structural maintenance of chromosome protein
substrate-binding region of ABC-type glycine betaine transport system
succinate-CoA ligase (ADP-forming), beta chain
succinate dehydrogenase/fumarate reductase iron-sulfur subunit
sulfate/molybdate ABC-transporter homolog, ATPase subunit
TetR family transcriptional regulator Member
thiamine pyrophosphate dependent enzyme related to acetolactate synthase
transcription factor TFIIS:DNA-directed RNA polymerase, M/15 kDa subunit
transcription initiation factor 2B subunit I
transcription initiation factor E subunit alpha
translation factor specialized for selenocysteine insertion
translation initiation factor IF-2 subunit alpha
translation initiation factor IF-2 subunit beta
translation initiation factor IF-2 subunit gamma
tungsten containing formylmethanofruran dehydrogenase subunit C-related protein
tungsten containing formylmethanofuran dehydrogenase, subunit A
tungsten containing formylmethanofuran dehydrogenase subunit B
tungsten containing formylmethanofuran dehydrogenase, subunit C
tungsten containing formylmethanofuran dehydrogenase, subunit D
tungsten containing formylmethanofuran dehydrogenase, subunit F
tungsten containing formylmethanofuran dehydrogenase, subunit G
tungsten containing formylmethanofuran dehydrogenase, subunit H
uncharacterized endonuclease III related protein
undecaprenyl pyrophospahte synthetase related protein (di-trans-poly-cis-decaprenylcistransferase)
vanadium nitrogenase-associated related protein N
xylose isomerase domain protein TIM barrel
Zn-finger, ZPR1 type:Zn-finger, ZPR1-related type