BLAST® settings vary by program and are chosen when searching for similar sequences. These are the options available in the Settings windows with applicable values, definitions, and usage tips.
Unless indicated otherwise, parameters apply to all programs.
Parameter and Program(s) | Valid Values | Explanation / Usage Tips | ||||||||||||||||
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Search Sensitivity |
Values from left to right are:
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Move the slider from left to right to yield larger answer sets. This adjusts the Expectation value from lower to higher, yielding less stringent matches (and therefore more answers). Default: Expectation value 10 (center of scale) Short query sequences: Increasing the E value may help when searching short sequences. |
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Show Additional Options |
Check box cleared (default) |
No additional options display. |
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Selected (check mark visible) |
Additional options display. |
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Basic Options |
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Low Complexity Filtering |
Selected (default) |
Applies a low complexity filter to your query. Short query sequences: Removing the filter may help when searching with short query sequences or sequences with large regions of low complexity. |
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Check box cleared | Filtering not applied. | |||||||||||||||||
Query Genetic Code
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Standard (default) |
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Between 1 and the maximum value indicated in the drop-down box. Default value is 25. |
You can also type a value up to the maximum. |
These parameters display when Show Additional Options is selected. Parameters and values are dependent on the BLAST program being used.
Parameter and Program(s) |
Valid Values |
Explanation / Usage Tips |
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Any positive number. Preset values
are: |
May range from large to very small, but always greater than 0. Increasing the number yields more, less stringent matches. Short query sequences: Increasing the E value may help when searching short sequences. |
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Word Size |
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You should rarely need to change the default, with these exceptions:
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Weight Matrix
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PAM-30 |
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Gap Cost
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Example for BLOSUM-62: Preset pair values for the Open/Extend cost are:
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Values will vary depending on Weight Matrix chosen. Other Weight Matrices available include; PAM-30, PAM-70, BLOSUM-45 and BLOSUM-80. |
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Open
Gap Cost
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Any number greater than 0. Default: 5, 2 NOTE: Whole numbers only, no decimals, fractions or ranges. |
These two values may be set independently (they do not need to be set as a pair) for BLASTn. |
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Penalty for Mismatch
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Any number less than 0 NOTE: Whole numbers only, no decimals, fractions or ranges. |
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Reward for Match
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1(default) - 8 NOTE: Whole numbers only, no decimals, fractions or ranges. |
Used (instead of weight matrices) to determine the score value for BLASTn searches. |
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