Related Material (VI) Identifying Motifs, Functional elements, Sites in Nucleic Acid Sequence (under construction)

Methods:pattern search, wt. matrix search

Databases: tfd, tfsites, profiles, imd matrix (selected example: CytR) - not connected

Important Features on a gene

  1. Promoters: FitConsensus, Profile analysis in GCG
  2. Terminators: Terminator in GCG
  3. Ribosome binding sites: GeneMark
  4. Signal peptide: SpScan in GCG
  5. Helix-turn-helix motif: HthScan in GCG
  6. Coiled coil motif: CoilScan in GCG

Tools (Pattern search tools)

Pattern search tools

  1. Motifs in GCG

    1. Purpose: Search for known protein sites in a given sequence
    2. Application: look for
    3. Algorithm: Pattern search
    4. Data file required: prosite.patterns (105 Kbytes)
    5. Related network tools: ProSiteScan, SignalScan
  2. Map in GCG (VectorNTI provide a better interface)

    1. Purpose: Search for known nucleic acid sites in a given sequence
    2. Application: Look for transcription factor binding sites in the upstream sequences
    3. Algorithm: Pattern search
    4. Data file required: tfsites.dat (694 Kbytes)
    5. Tricks in using this program
      • %fetch tfsites.dat enzyme.dat <=== Important!
      • %map
  3. Consensus / FitConsensus in GCG

Weight matrix search tools

  1. ProfileScan in GCG

  2. Terminator in GCG

  3. CoilScan in GCG

  4. HthScan in GCG

  5. SpScan in GCG

  6. IMDScan (A local example IMDScan screen)

  7. SignalScan (A local example of SignalScan)

Sequence database search tools in GCG

  1. ProfileSearch in GCG (part of the Profile Analysis)

  2. FindPatterns in GCG

Utilities

  1. Window / Statplot in GCG

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