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BLAST Settings

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

Additional Option Presets

Search Sensitivity

Search sensitivity slider

Values from left to right are:

Tick Mark 1 2 3 4 5 6 7
E value 1e-4 0.01 1 10 50 100 1,000

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.

Show Additional Options

Check box cleared (default)

No additional options display.

Selected (check mark visible)

Additional options display.

Basic Options

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.

Check box cleared Filtering not applied.

Query Genetic Code

  • BLASTx and tBLASTx only

Standard (default)
Vertebrate Mitochondrial
Yeast Mitochondrial
Mold Mitochondrial
Invertebrate Mitochondrial
Ciliate Nuclear
Echinoderm Mitochondrial
Euplotid Nuclear
Bacterial
Alternative Yeast Nuclear
Ascidian Mitochondrial
Flatworm Mitochondrial
Blespharisma Macronuclear

 

Max No. of Answers

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.

Advanced Options

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

Expectation Value

Any positive number. Preset values are:
1e -4
0.01
1
10 (default)
50
100
1000

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.

Word Size
  • BLASTn: 7 - 23 (default 11)
  • All other programs: 2 or 3 (default 3)

You should rarely need to change the default, with these exceptions:

  • Decreasing word size may help when searching short sequences.

  • Increasing word size may be needed to get queries with very long sequences to run to completion.

Weight Matrix

  • All programs except BLASTn

PAM-30
PAM-70
BLOSUM-80
BLOSUM-62 (default)
BLOSUM-45

Suggestions:

  • Use BLOSUM-62 to detect most weak protein similarities.

  • BLOSUM-45 for particularly long and weak alignments.

  • Other suggestions:

  • Query length Matrix Gap Costs
    <35 PAM-30 ( 9, 1)
    35 - 50 PAM-70 (10, 1)
    50 - 85 BLOSUM-80 (10, 1)
    85 BLOSUM-62 (11, 1)
    >85 BLOSUM-45 (15, 2)
Gap Cost
  • Values are set in pairs for tBLASTn, BLASTx, and BLASTp

Example for BLOSUM-62: Preset pair values for the Open/Extend cost are:

Open:

Extend:

6

2

7

2

8

2

9

1 or 2

10

1 or 2

11

1 default

11

2

12

1

13

1

Values will vary depending on Weight Matrix chosen. Other Weight Matrices available include; PAM-30, PAM-70, BLOSUM-45 and BLOSUM-80.

Open Gap Cost
Extend Gap Cost

  • BLASTn only

Any number greater than 0 - whole numbers only, no decimals, fractions or ranges.

Default: 5, 2

These two values may be set independently (they do not need to be set as a pair) for BLASTn.

Penalty for Mismatch

  • BLASTn only

Any number less than 0 - whole numbers only, no decimals, fractions or ranges.

 

Reward for Match

  • BLASTn only

1(default) - 8

Used (instead of weight matrices) to determine the score value for BLASTn searches.

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