---
name: "Bio::Tools::Gel"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.2-3"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tools::Gel"
---

# Bio::Tools::Gel(3pm)

Calculates relative electrophoretic migration distances

## NAME

Bio::Tools::Gel - Calculates relative electrophoretic migration distances

## SYNOPSIS

```
    use Bio::PrimarySeq;
    use Bio::Restriction::Analysis;
    use Bio::Tools::Gel;
    # get a sequence
    my $d = 'AAAAAAAAAGAATTCTTTTTTTTTTTTTTGAATTCGGGGGGGGGGGGGGGGGGGG';
    my $seq1 = Bio::Seq->new(-id=>'groundhog day',-seq=>$d);
    # cut it with an enzyme
    my $ra=Bio::Restriction::Analysis->new(-seq=>$seq1);
    @cuts = $ra->fragments('EcoRI'), 3;
    # analyse the fragments in a gel
    my $gel = Bio::Tools::Gel->new(-seq=>\@cuts,-dilate=>10);
    my %bands = $gel->bands;
    foreach my $band (sort {$b <=> $a} keys %bands){
      print $band,"\t", sprintf("%.1f", $bands{$band}),"\n";
    }
    #prints:
    #20   27.0
    #25   26.0
    #10   30.0
```

## DESCRIPTION

This takes a set of sequences or Bio::Seq objects, and calculates their respective migration distances using:\
     distance = dilation \* (4 - log10(length(dna));

Source: Molecular Cloning, a Laboratory Manual. Sambrook, Fritsch, Maniatis.  CSHL Press, 1989.

Bio::Tools::Gel currently calculates migration distances based solely on the length of the nucleotide sequence.  Secondary or tertiary structure,  curvature, and other biophysical attributes of a sequence are currently  not considered.  Polypeptide migration is currently not supported.

## 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 - Allen Day

Email allenday@ucla.edu

## APPENDIX

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

### new

```
 Title   : new
 Usage   : my $gel = Bio::Tools::Gel->new(-seq => $sequence,-dilate => 3);
 Function: Initializes a new Gel
 Returns : Bio::Tools::Gel
 Args    : -seq      => Bio::Seq(s), scalar(s) or list of either/both
                        (default: none)
           -dilate   => Expand band migration distances (default: 1)
```

### add\_band

```
 Title   : add_band
 Usage   : $gel->add_band($seq);
 Function: Calls _add_band with a (possibly created) Bio::Seq object.
 Returns :
 Args    : Bio::Seq, scalar sequence, or list of either/both.
```

### \_add\_band

```
 Title   : _add_band
 Usage   : $gel->_add_band($seq);
 Function: Adds a new band to the gel.
 Returns :
 Args    : Bio::Seq object
```

### dilate

```
 Title   : dilate
 Usage   : $gel->dilate(1);
 Function: Sets/retrieves the dilation factor.
 Returns : dilation factor
 Args    : Float or none
```

### bands

```
 Title   : bands
 Usage   : $gel->bands;
 Function: Calculates migration distances of sequences.
 Returns : hash of (seq_id => distance)
 Args    :
```

### log10

```
 Title   : log10
 Usage   : log10($n);
 Function: returns base 10 log of $n.
 Returns : float
 Args    : float
```