BioPerl

BioPerl

BioPerl is a collection of Perl classes to deal with biological information. It’s main application are parsing the diverse file types that occur in bioinformatics, and to provide standardized calls to bioinformatics tools.

Here, we will see how we can use BioPerl to parse different types of sequence files, alignment files, and annotation data.

Using BioPerl to deal with sequence

Biological sequence data formats

Many different types of sequence data formats exist, for different purposes, and providing different types of metadata.

The most common formats are:

fasta
genbank format
fastq
swissprot

Alignments

Annotation data