Pattern search and discovery, HMM

• Pattern discovery
• HMM (Hidden Markov Models)
• Other programs

• Pattern discovery

PFTOOLS

• pftools: Profile tools.




CONSENSUS

• consensus: Identification of consensus patterns in unaligned sequences.




PRATT

• pratt: Patterns discovery in sets of unaligned protein sequences.




SMILE

• smile: Structured Motif Inference and Evaluation.




EMBOSS

• prophet: Gapped alignment for profiles.

• HMM (Hidden Markov Models)

  HMMER

  • hmmalign: Align sequences to an existing model.
  • hmmbuild: Builds a HMM from a multiple sequence alignment.
  • hmmcalibrate: Takes an HMM and empirically determines parameters that are used to make searches more sensitive, by calculating more accurate expectation value scores (E-values).
  • hmmconvert: Convert a model into different formats.
  • hmmemit: Emit sequences probabilistically from a profile HMM.
  • hmmfetch: Get a single model from an HMM database.
  • hmmpfam: Search an HMM database for matches to a query sequence.
  • hmmsearch: Search a sequence database for matches to an HMM.

• Other programs

SAPS

• saps: Statistical Analysis of Protein Sequences.




EMBOSS

• msbar: Mutate sequence beyond all recognition.
• compseq: Counts the composition of dimer/trimer/etc words in a sequence.
• shuffleseq: Shuffles a set of sequences maintaining composition.
• chaos: Create a chaos game representation plot for a sequence.
• freak: Residue/base frequency table or plot.