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 | = 500000Â 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 -150Â bp | No | No | No | JASPAR, TRANSFAC | PScanChIP | Used existing Pscan algorithm | Yes | Yes | No | No | No | 2013 | 1.0 | [3] |