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GELBANK


NAR Molecular Biology Database Collection entry number 222
Babnigg G., Giometti C.S.
Argonne National Laboratory Biosciences Division Protein Mapping Group Argonne, IL 60439, USA

Database Description

GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel images of proteomes from organisms with known genome information (available at http://gelbank.anl.gov). GELBANK serves as a database for those proteomics labs that do not want to set up their own website for the presentation of their 2DE gel patterns and for those labs that would like to share their data with other researchers in the field. The most widely used separation method for proteome analysis is currently two-dimensional gel electrophoresis (1), where the proteins are separated according to their isoelectric point (pI) in the first dimension and their molecular weight (MW) in the second dimension. Using protein specific dyes that are stoichiometric with respect to the optical density of the dye and the abundance of the protein, the relative abundance of each protein detected in a 2DE pattern can be determined (2, 3). Using calibration proteins, these 2DE gel patterns provide information of relative abundance, MW and pI of isolated proteins in the given pI and MW range. The stained protein spots can be analyzed by peptide mass fingerprinting. GELBANK currently includes 90 completed genomes available from the National Center for Biotechnology Information (NCBI). A web interface allows the upload of 2 DE gel patterns and their annotation for registered users. The images are organized by species, tissue type, separation method, sample type, and staining method. The database can be queried based on these attributes. A web interface allows registered users to assign molecular weight and pH gradient profiles to their own 2DE gel patterns as well as link protein identifications to a given spot on the pattern. The website presents all of the submitted 2DE gel patterns where the end-user can dynamically display the images or parts of images along with both molecular weight and pH profile information and linked protein identification. A collection of images can be selected for the creation of animations where the user can select sub-regions of interest from an unlimited number of 2DE gel patterns for visualization. The website also presents simple search engines for the querying of proteomes based on annotation data, molecular weight, isoelectric point (pI), and sequence pattern. If the protein has been linked with a given 2DE gel pattern, a link to the associated pattern(s) is presented. Titration curves of a given sequence or a collection of sequences can be generated and a utility is provided that dynamically calculates the isoelectric point of a given protein sequence by 'turning' on and off those amino acids affecting it. The website also presents a web-interface to the multiple sequence alignment tool Clustal W (4). GELBANK presents a unique capability: BIO-BAG. BIO-BAG allows users to store various objects (e.g. sequences, 2DE gel patterns, and image animations) while browsing the website. The content of BIO-BAG is permanent for those users who register and log-in into the system. BIO-BAG provides a simple interface for tools that are pertinent to the given objects, such as alignment of protein sequences, protein titration curve(s), image animations, etc.

Acknowledgements

This work was supported by the Office of Biological and Environmental Research through the Microbial Genome Project, U.S. Department of Energy, under Contract No. W-31-109-ENG-38.

References

1. O'Farrell, P.Z. and Goodman, H.M. (1976) Resolution of simian virus 40 proteins in whole cell extracts by two-dimensional electrophoresis: heterogeneity of the major capsid protein. Cell 9, 289-298
2. Anderson, L.A., Nance, S., Tollaksen, S.L., Giere, F.A., and Anderson, N.G. (1985) Quantitative reproducibility of measurements from Coomassie Blue-stained two-dimensional gels: Analysis of mouse liver protein patters and a comparison of BALB/c and C57 strains. Electrophoresis 6, 592-599
3. Giometti, C.S., Gemmell, M.A., Tollaksen, S.L. and Taylor, J. (1991) Quantitation of human leukocyte proteins after silver staining: A study with two-dimensional electrophoresis. Electrophoresis 12, 536-543
4. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680


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