MEET (version 5.1.1)

iicc: A set of initial conditions

Description

A set of initial conditions for the MEET-package

Arguments

TF

A set of nucleotide sequences

nameTF

Transcription Factor name

seqin

Candidate sequence

alg

A set of Multiple Sequence Alignment

method

A set of motif discovery algorithms

mode

Training or detection

org

Background organism

vector

Characteristic parameters methodfor leave-one-out cross-validation.

num_motif

Number of motif

len_motif

Length of motif

direction

Forward, reverse or both

threshold

P-value

order

Renyi Order

model

model

position

Binding site position for training

mv

missing values

gapopen

The gap open score

maxiters

Maximum number of iterations

gapextend

The gap extend score

optionsFile

Path for MEME/MAST, clustalw and muscle

Details

Models (Entropy, Divergence and Qresiduals) for a set of TFBS. Homo sapiens:AP1,CREB1,E2F1,ELK1,ELK4,ESR1,ETS1,FEV,FOXD1,FOXO3,HLF,INSM1,Irf_2,MAX,MYC_MAX,MZF1_1_4,MZF1_5_13,NFATC2,NFE2L2,NFIL3,NFKB1,NF_kappaB,NKX3_1,NR3C1,NRF21,PPARG,Pax6,RORA_1,RORA_2,RREB1,REL,RELA,REST,RXRA_VDR,SP1,SPIB,SRF,SRY,STAT1,TLX1_NFIC,TAL1_TCF3,YY1,ZNF354C. Rattus norvegicus:AP1,CREB1,Ddit3_Cebpa,FEV,Foxd3,Foxq1,Mafb,NFATC2,NF_kappaB,NR3C1,SP1. Mus musculus:AP1,CREB1,Ddit3_Cebpa,FEV,Foxd3,Foxq1,Mafb,NFATC2,NF_kappaB,NR3C1,SP1. Drosophila melanogaster:Abd_B,Antp,Awh,B_H1,B_H2,C15,CG11085,CG11294,CG11617,CG13424,CG15696,CG32105,CG32532,CG42234,CG4328,CG7056,CG9876,Deaf1,Dfd,Dll,Dr,E5,HGTX,Hmx,Kr,Lag1,Lim1,Lim3,NK7_1,Oct,PHDP,Pph13,Ptx1,Ptx1,Rx,Six4,Vsx1,Vsx2,a1,abd_A,achi,ap,ara,bcd,brk,bsh,btd,btn,cad,caup,ct,dl_1,ems,en,eve,exd,exex,fkh,ftz,gt,h,hbn,hkb,hth,ind,inv,kni,lab,lbe,mirr,nub,oc,odd,onecut,opa,otp,pan,pb,ro,sd,slbo,slou,slp1,sna,so,tin,tll,tup,twi,unc_4,unpg,usp,vis,vnd,vvl,zen,Gsc,dl_2,ttk,repo,Scr