Developments in CORG: a gene-centric comparative genomics resource

The CORG resource (Comparative Regulatory Genomics, ) provides extensive cross-species comparisons of promoter regions in particular and whole gene loci in general. Pairwise as well as multiple alignments of 10 vertebrate species form the key component of CORG. We implemented a rapid alignment approach based on weight matrix motif anchors to ensure efficient computation and biologically informative alignments. All CORG workbench components have been enhanced towards more flexibility and interactivity. Reference sequence based data presentation and analysis was put into the well-known and modular Generic Genome Browser framework. Herein, various plugins facilitate online data analysis and integration with static conservation data. Main emphasis was put on the design of a new JAVA WebStart application for comparative data display. Flexible data import and export options for standard formats complete the provided services

Hardware Software Co-Design for Protein Identification

Recently new technologies and research in computational bioinformatics have revolutionized the rate of biological data generation. A vast amount of proteomics and genomics data is contributed to the life science society by researchers especially in the domain of high throughput next generation sequencing methods and it is doubling at every 18 months. Protein identification is a fundamental step in protein sequence analysis and it needs efficient solutions to match the data growth. Rapid methods are focused in the quest for faster protein sequence analysis to scan databases and identify a protein accurately. This benefits the discipline of disease biomarker identification and aid disease diagnosis and prognosis

SITEBLAST - rapid and sensitive local alignment of genomic sequences employing motif anchors

MOTIVATION: Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications of local alignment algorithms (e.g. phylogenetic footprinting) would benefit from including prior knowledge (e.g. binding site motifs) in the alignment building process. RESULTS: We introduce predefined sequence patterns as anchor points into a heuristic local alignment strategy. We extended the BLASTZ program for this purpose. A set of seed patterns is either given as consensus sequences in IUPAC code or position-weight-matrices. Phylogenetic footprinting of promoter regions is one of many potential applications for the SITEBLAST software. AVAILABILITY: The source code is freely available to the academic community from http://corg.molgen.mpg.de/softwar