FastaTweaseEvaluationProtocol

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Evaluation protocol for FastaTwease

Aims

An evaluation of FastaTwease should determine how well FastaTwease compares to established bioinformatics methods for sequence comparison. The evaluation has the following aims:

  1. Compare quality of results with an array of established methods, including:
    • megablast
    • BLAST
    • Exact Smith-Waterman (e.g., BLITZ server at EBI or equivalent)
    • PSI-BLAST
    • Threading methods (even though these require 3D structures for the target and FastaTwease has no such limitation).
  2. Compare the efficiency of the method with the methods listed under point 1 above.
    • Evaluate query performance with respect to length of query and size of corpus.
  3. Compare with easy and difficult targets.

Easy targets

Easy targets are sequences that are similar to the target query and can be located with megablast, BLAST, or exact Smith-Waterman with no ambiguity. Easy targets match the query with E-values below 1E-3.

Hard Targets

Previous work

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