BMC Genomics Database Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (CyMoBase) Florian Odronitz and Martin Kollmar* BioMed Central Open Access Address: Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany Email: Florian Odronitz - flod@nmr.mpibpc.mpg.de; Martin Kollmar* - mako@nmr.mpibpc.mpg.de * Corresponding author Published: 29 November 2006 BMC Genomics 2006, 7:300 doi:10.1186/1471-2164-7-300 This article is available from: http://www.biomedcentral.com/1471-2164/7/300 Received: 27 June 2006 Accepted: 29 November 2006 © 2006 Odronitz and Kollmar; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Annotation of protein sequences of eukaryotic organisms is crucial for the understanding of their function in the cell. Manual annotation is still by far the most accurate way to correctly predict genes. The classification of protein sequences, their phylogenetic relation and the assignment of function involves information from various sources. This often leads to a collection of heterogeneous data, which is hard to track. Cytoskeletal and motor proteins consist of large and diverse superfamilies comprising up to several dozen members per organism. Up to date there is no integrated tool available to assist in the manual large-scale comparative genomic analysis of protein families. Description: Pfarao (Protein Family Application for Retrieval, Analysis and Organisation) is a database driven online working environment for the analysis of manually annotated protein sequences and their relationship. Currently, the system can store and interrelate a wide range of information about protein sequences, species, phylogenetic relations and sequencing projects as well as links to literature and domain predictions. Sequences can be imported from multiple sequence alignments that are generated during the annotation process. A web interface allows to conveniently browse the database and to compile tabular and graphical summaries of its content. Conclusion: We implemented a protein sequence-centric web application to store, organize, interrelate, and present heterogeneous data that is generated in manual genome annotation and comparative genomics. The application has been developed for the analysis of cytoskeletal and motor proteins (CyMoBase) but can easily be adapted for any protein. Background The success of the genome sequencing projects have cul- minated in release 149 of GenBank [1] that announced two milestones: the total sequence data passed the 100 gigabases mark, and, for the first time, the number of bases derived from whole genome shotgun sequencing projects exceeded the number of bases in the traditional divisions of GenBank. However, the process of genome annotation still lags considerably behind that of genome data generation. Although many tools have been devel- oped for the ab initio annotation of whole genomes, espe- cially the annotation of data from higher eukaryotes yields low success rates [2]. The success rates can consider- ably be increased by similarity searches of EST data or of annotated data from other genomes. But also these data have their drawbacks: ESTs are fragmentary and might suf- Page 1 of 8 (page number not for citation purposes)