---
name: "Bio::Matrix::Scoring"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Matrix::Scoring"
---

# Bio::Matrix::Scoring(3pm)

Object which can hold scoring matrix information

## NAME

Bio::Matrix::Scoring - Object which can hold scoring matrix information

## SYNOPSIS

```
  use Bio::Matrix::Scoring;
```

## DESCRIPTION

An object which can handle AA or NT scoring matrix information.  Some transformation properties are available too.

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and  reponsive experts will be able look at the problem and quickly  address it. Please include a thorough description of the problem  with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### new

```
 Title   : new
 Usage   : my $obj = Bio::Matrix::Scoring->new();
 Function: Builds a new Bio::Matrix::Scoring object
 Returns : an instance of Bio::Matrix::Scoring
 Args    :
```

### entropy

```
 Title   : entropy
 Usage   : $obj->entropy($newval)
 Function:
 Example :
 Returns : value of entropy (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### expected\_score

```
 Title   : expected_score
 Usage   : $obj->expected_score($newval)
 Function:
 Example :
 Returns : value of expected (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### scale

```
 Title   : scale
 Usage   : $obj->scale($newval)
 Function:
 Example :
 Returns : value of scale (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### scale\_value

```
 Title   : scale_value
 Usage   : $obj->scale_value($newval)
 Function:
 Example :
 Returns : value of scale_value (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### description

```
 Title   : description
 Usage   : $obj->description($newval)
 Function:
 Example :
 Returns : value of description (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### database

```
 Title   : database
 Usage   : $obj->database($newval)
 Function:
 Example :
 Returns : value of database (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### lowest\_score

```
 Title   : lowest_score
 Usage   : $obj->lowest_score($newval)
 Function:
 Example :
 Returns : value of lowest_score (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### highest\_score

```
 Title   : highest_score
 Usage   : $obj->highest_score($newval)
 Function:
 Example :
 Returns : value of highest_score (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### lambda

```
 Title   : lambda
 Usage   : $obj->lambda($newval)
 Function:
 Example :
 Returns : value of lambda (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### H

```
 Title   : H
 Usage   : $obj->H($newval)
 Function:
 Example :
 Returns : value of H (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```