Scoring options

These are the following 2 scoring options which can be selected:

• The local/global options determine how the model and sequence are matched with each other. Local refers to a part of the model or sequence, whereas global refers to the whole. Local/local matching (default) will find the highest-scoring match of any part of the model to any part of the sequence. Global/global matching will return the score for the whole sequence to the whole model. This is useful when you know that your query sequence should match exactly one domain. Local/global matching will find the best score of any part of the model to the whole sequence. This is useful for scoring sequence fragments.

• The blast pre-search is to filter out obvious high-scoring hits which need not be run against the more sensitive but computationally expensive HMM library. This option can be turned off completely, which may be useful in cases where blast is making false high-scoring hits. This is known to be possible with sequences containing low-complexity or short-repeat regions.