Protein Analysis

Pattern & Motif Searching

• ADDA: Automatic Domain Decomposition Algorithm
  A database of protein domain families with complete coverage of all protein sequences
• BLOCKS
  The Blocks server provides tools for the detection and verification of protein sequence homology. Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins
• eBlocks
  Search for ungapped alignments of highly conserved regions among a protein family or superfamily
• EMBL-EBI FingerPRINT Scan
  FingerPRINT Scan identifies PRINTS sequence motif patterns within a protein sequence
• EMBL-EBI InterProScan
  Identify protein family (and DNA) domains, patterns, motifs, protein families, and functional sites
• EMBL-EBI Pratt
  Search for patterns conserved in sets of unaligned protein sequences
• Meta-MEME
  Build and use motif-based hidden Markov models of DNA and proteins
• NCBI CDD: Conserved Domain Database
  A compilation of multiple sequence alignments of evolutionarily conserved protein domains, linked to sequence and stucture data
• PRINTS
  Search for protein fingerprints
• ProDom
  Search protein families and domains
• PROSITE
  Identify protein families and domains for a given protein sequence
• SMART
  Identify and annotate genetically mobile domains and domain architectures