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.

More information about the format can be found at 
http://useq.sourceforge.net/useqArchiveFormat.html. 

Useq files may be generated using tools in the USeq package, available at 
http://useq.sourceforge.net. They may be generated from 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.

To see a practical implementation of Bio::DB::USeq, see the collection of 
data analysis scripts in the Bio::ToolBox package, available from your 
local CPAN mirror and at http://biotoolbox.googlecode.com.