iicc: A set of initial conditions

In MEET: MEET: Motif Elements Estimation Toolkit

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

Author(s)

Erola Pairo <epeiroatibec.pcb.ub.es> and Joan Maynou <joan.maynouatupc.edu>.

MEET documentation built on May 2, 2019, 1:45 p.m.