Structural Biology

	We have developed a protein sequence identifier (SEGUID) based on the Secure Hash Algorithm (SHA-1) digest of the primary sequence because our bioinformatics, analytical, and high-throughput proteomics pipelines suffered from changing and disappearing protein identifiers. A SEGUID is stable for the lifetime of a protein and is used as the central identifier while all other aliases are treated as dynamic properties. Everyone can derive the same SEGUID from the sequence information, which allows easy data sharing. The use of SEGUID ensures that proteomics data is resilient to changes in annotation databases and the reports generated reflect the most recent annotations collected from sequence databases. Our SEGUID website provides a number of web applications and web services which are described in this manuscript. The FTP site provides pre-calculated data, FASTA files, alias tables, and sample programs describing the web services and their consumption by other applications.

	We have developed various tools to interact with the SEGUID database. The user can quickly find protein sequence aliases, identifiers, and annotations in publicly available databases.

	Various tools have been developed to support structural genomics efforts: sequence manipulation, sequence analysis, primer design, and data manipulation.

	Intranet applications supporting structural genomics experiments (cloning, purification, and crystallization LIMS).

	GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel patterns of proteomes from organisms with known genome information (available at http://gelbank.anl.gov and ftp://bioinformatics.anl.gov/gelbank/). It includes completed, mostly microbial proteomes available from the National Center for Biotechnology Information. A web interface allows the upload of 2D 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 protein or 2DE-pattern attributes. A web interface allows registered users to assign molecular weight and pH gradient profiles to their own 2D gel patterns as well as to link protein identifications to a given spot on the pattern. The website presents all of the submitted 2D gel patterns where the end-user can dynamically display the images or parts of images along with molecular weight, pH profile information and linked protein identification. A collection of images can be selected for the creation of animations from which the user can select sub-regions of interest and unlimited 2D gel patterns for visualization. The website presents identifications for more than 80 gel patterns for Homo sapiens, Methanococcus jannaschii, Pyro coccus furiosus, Shewanella oneidensis, Escherichia coli and Deinococcus radiodurans.

	Intranet application for the query of mass spectrometry data.

	Intranet applications supporting two-dimensional gel electrophoresis experiments (LIMS).

	Intranet applications supporting the analysis of two-dimensional gel electrophoresis experiments (LIMS).

	The SOAP-Match web service is designed to search a number of protein databases for a pattern using Regular Expressions (REGEX).


.NET Applications

	The purpose of ANLProImage.a.NET is compare two proteomics images resulting from a two-dimensional electrophoresis. The individual images can be adjusted for brightness and contrast using two different methods. The resulting two gray scale images can be compared by converting them to differing color spaces (either white or black background) and overlaying the two pseudo-images. In order to reveal local similarities or differences, the images can be repositioned. The manipulated individual images and the combined image can be saved in three different formats, such as jpeg as a reference case or for future comparisons.

	BioBLAST is a .NET desktop GUI for the BLAST Windows executable (blastpgp for protein similarity searches). It uses web services to maintain an up-to-date copy of the BLAST executable, protein sequence databases, and the BioBLAST assembly itself. The user can select which protein databases to download. The command line arguments of blastpgp are available per user request. Preferences and BLAST run statistics are stored as XML files for compatibility with other applications. All parameters and statistics can be recalled for each BLAST run. The intent is to run BioBlast off a laptop computer with Microsoft Windows XP operating system.

	The purpose of ANLThinUpdates.a.NET is an executable application that will automatically update applications of the toolkit. The advantage of this software is that it provides very fast updates, there are no reminders needed so that updates are done automatically, and there is no need to reboot the computer.

	The purpose of AnlWs4Big, Ver. 1.0, is to transfer or download large, gigabyte sized, bioinformatics and proteomics files across the web. The BIO Division .NET applications use web services (SOAP internet protocol) and the researchers needed a way to transfer these files. The user can specify the “packet” size that the data blocks can be downloaded easily. These downloads are generally going to a laptop (with Windows). AnlWs4Big was specifically developed for any type of data stored in Oracle 10g or above databases.