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Bio::DB::USeq - An adaptor for parsing USeq data files
INTRODUCTION
Bio::DB::USeq is a BioPerl style adaptor for reading useq files. Useq files are
compressed, indexed, binary data files supporting modern bioinformatic datasets,
including genomic points, scores, and intervals. As such, they can be used as a
replacement for text Wig and BED file formats. They may be used natively by the
Integrated Genome Browser (IGB) and DAS/2 servers.
USeq files are typically half the size of corresponding bigBed and bigWig files,
due to a compact internal format and lack of internal zoom data. This adaptor,
however, can still return statistics across different zoom levels in the same
manner as big files, albeit at a cost of calculating these in realtime.
More information about the format can be found at
Useq files may be generated using tools in the USeq package, available at
native Bar files, text Wig files, text Bed files, and UCSC bigWig and bigBed
file formats.
COMPATIBILITY
The adaptor follows most conventions of other BioPerl-style Bio::DB
adaptors. Observations or features in the useq file archive are
returned as SeqFeatureI compatible objects.
Coordinates consumed and returned by the adaptor are 1-based, consistent
with BioPerl convention. This is not true of the useq file itself, which
uses the interbase coordinate system.
Unlike wig and bigWig files, useq file archives support stranded data,
which can make data collection simpler for complex experiments.
GBrowse compatibility is fully supported. It will work with the segments
glyph for intervals, the wiggle_xyplot glyph for displaying mean scores,
and the wiggle_whiskers glyph for displaying detailed statistics. For
stranded quantitative data sets, two graphs will be generated for each
strand.
LIMITATIONS
This adaptor is read only. USeq files in general are not modified or
written, although chromosome specific statistics may be written to
the metadata for persistence.
No support for genomic sequence is included. Users who need access to
genomic sequence should seek an alternative BioPerl adaptor, such as
Bio::DB::Fasta.
Useq files do not have the concept of type, primary_tag, or source
attributes, as expected with GFF-based database adaptors. However,
special feature types are supported, including binned wiggle
and summary features, for data access.
INSTALLATION
Bio::DB::USeq requires the installation of BioPerl and Archive::Zip.
Install Bio::DB::USeq using the standard incantation.
perl ./Build.PL
./Build
./Build test
./Build install
IMPLEMENTATION
Read the Bio::DB::USeq POD documentation for usage, API details, and
GBrowse configuration.
The included script, USeqInfo.pl, provides basic information about
USeq archives, including metadata, chromosome information, and genome-wide
score statistics. It also demonstrates a practical application of using
the Bio::DB::USeq module.
To see a practical implementation of Bio::DB::USeq for use in data
analysis, see the collection of scripts in the Bio::ToolBox package,
available from your local CPAN mirror and at