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BioMed Research International
Volume 2014, Article ID 893501, 5 pages
Research Article

AmalgamScope: Merging Annotations Data across the Human Genome

1Bioinformatics and Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece
2Henley Business School, Business Informatics, University of Reading, Whiteknights, Reading RG6 6UD, Uk

Received 1 October 2013; Revised 21 February 2014; Accepted 18 April 2014; Published 20 May 2014

Academic Editor: Shigehiko Kanaya

Copyright © 2014 Georgia Tsiliki et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The past years have shown an enormous advancement in sequencing and array-based technologies, producing supplementary or alternative views of the genome stored in various formats and databases. Their sheer volume and different data scope pose a challenge to jointly visualize and integrate diverse data types. We present AmalgamScope a new interactive software tool focusing on assisting scientists with the annotation of the human genome and particularly the integration of the annotation files from multiple data types, using gene identifiers and genomic coordinates. Supported platforms include next-generation sequencing and microarray technologies. The available features of AmalgamScope range from the annotation of diverse data types across the human genome to integration of the data based on the annotational information and visualization of the merged files within chromosomal regions or the whole genome. Additionally, users can define custom transcriptome library files for any species and use the file exchanging distant server options of the tool.