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

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

Darwin Kernel Version 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386
David J Reiss, Institute for Systems Biology
cMonkey integrated biclustering algorithm for learning co-regulated gene modules
RCurl, foreach, doMC, multicore, ff, igraph, RSVGTipsDevice, hwriter, trimcluster

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

150-end, similar to phosphate hydrolising
ABC transporter (sulfate/molybdenum) permease subunit
ATP-dependent protease binding subunit ClpB
Cytadherence High Molecular Weight Protein 2 (SwissProt HMW2_MYCPN)
DNA helicase II (with Mycoplasma specific C-terminal domain)
DNA-directed RNA polymerase subunit alpha
DNA-directed RNA polymerase subunit beta
DNA-directed RNA polymerase subunit beta'
DNA-directed RNA polymerase subunit delta
Ferric uptake regulator (Koonin for MG homologue)
Glpq or Uplq glycerophosphoryl diester phosphodiesterase
Holliday junction DNA helicase motor protein
PEP-dependent HPr protein kinase phosphoryltransferase (Enzyme I)
PTS system mannitol-specific component IIA (EIIA-MTL)
PTS system, glucose-specific IIABC component
ParA family of ATPase involved in chromosome partition
Penicillin-binding protein-related factor A, putative recombinase
Probably ABC transporter membrane protein subunit
Psta /Pstc-like ABC transporter; phosphate specific
RNA helicase, eIF4-A translation initiation factor
SAM-Dependent Methytransferase (Koonin for MG ortholog)
SMC family, chromosome/DNA binding/protecting functions
Trk-type K+ transport systems, membrane components
Type I Restriction Enzyme hsdR (fragment)
ascorbate-specific PTS system enzyme IIC
aspartyl/glutamyl-tRNA amidotransferase subunit C-like protein
branched-chain alpha-keto acid dehydrogenase subunit E2
but only N- and C-term; inbetween (500AA) seg and coil
coiled coil protein, putative structural protein involved in cytosceleton
competence locus operon protein 3 homolog; similar to Swiss-Prot Accession Number P39695, from B. subtilis
conserved hypothetical protein, 154-190 similar to GTP/ATP binding proteins
conserved hypothetical protein, similar to reticulocyte binding protein
conserved hypothetical protein, suggestion: membrane transporter component
contains j-domain of DnaJ; and a domain common to cytadherence proteins
general amino acid permease GAP1 homolog; similar to Swiss-Prot Accession Number P19145, from S. cerevisiae
hemk family, similar to methyltransferase (S-adenosyl-methionine dependent)
high affinity transport system protein P37
hypothetical protein (yabC) homolog; similar to Swiss-Prot Accession Number P37544, from B. subtilis
hypothetical protein, involved in cytadherence
oligopeptide transport ATP-binding protein OppD
oligopeptide transport system permease protein AmiD
oligopeptide transport system permease protein OppB
osmotical inducible protein C like family; inducable by osmotic stress and by organic hydroperoxides
phosphate transport system regulatory protein
predicted metalloenzyme interacting with hemolysin
probably membrane component, similar to STARP antigen
protein phoshatase 2C homolog; similar to Swiss-Prot Accession Number P35182, from S. cerevisiae
putative inner membrane protein translocase component YidC
riboflavin kinase (flavokinase)/FMN adenylyltransferase (FAD pyrophosphorylase) (FAD synthetase); bifunctional
segregation and condensation protein A/unknown domain fusion protein
similar to ATP-dependent RNA helicase deaD
similar to NADP-dependent alcohol dehydrogenase
similar to PHOSPHOTRIESTERASE HOMOLOGY PROTEIN
similar to PP-loop superfamily ATPase/cell cycle protein MESJ homologues
similar to PTS system: EIIB and N-term part of EIIC; bidomainal
similar to RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D
similar to cobalt transport membrane protein
similar to nucelotidyl transferase/polynicleotide cleavage
similar to phosphate binding protein Psts
similar to phosphotransferase protein II, component A, for pentitol, SGAT homolog
similar to ribosomal S6 modification protein
similar to single stranded RNA(DNA) processing enzyme
similarity to pertussis toxin subunit s1
small GTPase ERA involved in regulating metabolism and cell division
sn-glycerol-3-phosphate transport system permease protein
specificity determining subunit for restriction enzyme belonging to the K family of S proteins
sugar (ribose/galactose) ABC transporter ATP-binding subunit
sugar (ribose/galactose) ABC transporter permease subunit
sugar (ribose/galactose) ABC transporter permease subunit, but probably C-terminal
tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
this protein specifications means only that it is a type I restriction with enzyme ecokI specificity protein
tlyC homolog, hemolysin activity doubtful
two functions are possible, as both enzyme are homologous to each other: phosphomannomutase or phosphoglucomutase
type I restriction enzyme ecokI specificity protein
type I restriction enzyme ecokI specificity protein (hsdS) homolog