[Bioperl-l] file format for alignment plus features for aligned sequences

[Scott Markel]

A question on behalf of the Discovery Studio group at Accelrys -

They have alignment data with annotations, e.g., visualization settings or alignment properties.  The aligned sequences also have features, e.g., domain boundaries or secondary structure motifs.  They currently use BSML to save sequences and features.

Is there an extension of BSML that can also save the alignment information?

Are there any good file formats that can be used to store an alignment plus features associated with the aligned sequences?

Are there other mailing lists that might be more appropriate for these questions?

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
San Diego, CA 92121                 fax:    +1 858 799 5222
USA                                 web:    http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Secretary, Board of Directors:
    International Society for Computational Biology
Chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics