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Table 1 A summary of motif finding web tools

From: A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

Web Tool Pipeline Accept File Format Maximum File Size Maximum Sequence Length P-Value Option Motif’s Size Option # of Motifs Option Ref. Database Web Tool Approach Ref. Database Option Ref. Genome Option Log in Required Email Required User Account Option Published Year Current Version Ref. #
MEME No Fasta = 60000 characters < 1000 bp No Yes Yes JASPAR, BLOCKS, UniProbe, …., user database MEME Implemented Multiple EM No No No Yes No 2006 4.9.1 [4]
GLAM2 No Fasta = 60000 characters = 10000 bp No No No JASPAR, UniProbe, …., user database GLAM2 Implemented novel Gapped Local Alignment of Motifs algorithm No No No Yes No 2008 4.9.1 [5]
CisFinder No Fasta, plain text delimited Unspecified = 50 Mb FDR option No Yes JASPAR, CisView, …., user database CisFinder Implemented novel CisFinder algorithm Yes No Optional Optional Optional 2009 Unspecified [6]
W-ChIPMotifs Yes Fasta Unspecified Unspecified No No No JASPAR, TRANSFAC, …., user database W-ChIPMotifs Used existing ChIPMotifs program and incorporated other existing tools: MEME, MaMF, and Weeder No Human and Mouse only No Yes No 2009 Unspecified [7]
CompleteMOTIFs Yes Bed, fasta, gff = 500000 bp for MEME, Weeder, = 5000000 for ChIPMunk Unspecified Yes Yes for MEME No JASPAR, TRANSFAC CompleteMOTIFs Integrated existing tools: MEME, Weeder, and ChIPMunk Yes Yes Optional Optional Optional 2011 Unspecified [8]
DREME No Fasta Unspecified Unspecified E-value option No No JASPAR, UniProbe, …., user database DREME Implemented novel Discriminative Regular Expression Motif Elicitation algorithm (DREME) No No No Yes No 2011 4.9.1 [9]
MEME-ChIP Yes Fasta Unlimited Unlimited E-value option Yes Yes JASPAR, UniProbe, …., user database MEME-ChIP Integrated existing tools: MEME and DREME No No No Yes No 2011 4.9.1 [10]
RSAT peak-motifs Yes Raw, multi, tab, fasta, wconsensus, IG Unlimited Unlimited No Yes Yes JASPAR, UniProbe, DMMPMM, RegulonDB, …, user database RSAT peak-motifs Implemented RSAT oligo-analysis, RSAT dyad-analysis, RSAT local-word analysis, MEME, ChlPMunk Yes No No Optional No 2012 Unspecified [11]
PScanChIP No Bed Unlimited 100 -150 bp No No No JASPAR, TRANSFAC PScanChIP Used existing Pscan algorithm Yes Yes No No No 2013 1.0 [3]