Sequence Homolog Searching

• Applications:
  • Search your new sequence against a database.
  • Search a known sequence against a new database or genome to look for new relatives.
• Suggested Methods:
  • BLAST Variants on BlastMachine
    • BLASTN - fast and often sufficient.
    • TBLASTX - More tolerant of sequence variation and frame-shifts, but slower

Remote Homolog Searching:

• Applications:
  • Find distant relatives of a gene or protein.
• Suggested Methods:
  • Smith-Waterman (GeneMatcher2) - More sensitive than BLAST when comparing highly diverged sequences, but much slower.
  • Double Frame Smith-Waterman (GeneMatcher2)- like TBLASTX above, it is more tolerant of sequence variation and frame-shifts. Very computationally intensive.

  • PSI-BLAST (BlastMachine) - Iteratively explore for distant members of a protein family.

  • Fugu genome (avail. on BlastMachine and GeneMatcher2) - The Fugu genome is very compact, and is the most evolutionarily distant vertebrate from humans that has been almost fully sequenced. It has been successfully used as a bridge to find distant human family members of a newly discovered human gene (internal Genome Center project).

  • Because Profile HMMs are a consensus-type model, they may be less useful for detecting very remote homologs than some other methods.

EST Annotation

• Applications:
  • Identify ESTs
• Suggested Methods:
  • BLASTN (BlastMachine).
  • TBLASTX (BlastMachine) - for cross-species EST identification, e.g. search non-human ESTs against the human or other gene databases.
  • Double-Affine Smith-Waterman - compare ESTs to genomic DNA. Separate penalties for large insertions make it intron tolerant.
    

Protein Domain Detection

• Applications:
  • Identify protein domains in a new sequence.
  • Search for new members of a particular domain.
  • Protein domain can imply function.
• Suggested Methods:
  • Hidden Markov Models such as the pfam library (GeneMatcher2).
  • Profile (PROSITE?)

Gene Finding

• Applications
  • Search new or unfinished sequences for new genes.
• Suggested Methods
  • Genewise (GeneMatcher2) - Genewise compares genomic sequences to protein reference sequences or HMM models at the protein level, allowing for introns (splicing) and frameshifts.

Optimal Alignment of Sequences

• Suggested Methods
  • Smith-Waterman (GeneMatcher2).               

Alignment of Short Sequences

• Suggested Methods
  • Fasta - fasta lies between BLAST and Smith-Waterman in accuracy and speed (on a given processor).  It can be used to find shorter matches than BLAST.