Genome Project Solutions

Genome Project Solutions, Inc. has extensive capabilities in bioinformatics, to include producing custom software, broad experience in high-throughput DNA sequencing, gene expression studies, and related molecular biology techniques, expertise in evolutionary and functional genomics, proteomics, developmental biology, and many other fields, and familiarity with the policies and programs of governmental and other funding agencies. This includes the applications of genomics research to areas such as biodefense, ecology, medicine, pharmacology, and agriculture.

Genome Project Solutions plays varying roles depending on the needs of each project. For some, we may simply provide advice on acquiring funding, planning and managing projects, or promoting particular genome projects at government agencies. For others, we may participate by providing one or a few discrete genomic or informatic products. For still others, we may establish and manage a large consortium of scientists for a complex project such as sequencing and analyzing a complete eukaryotic genome. Initial consultations are free of charge and commitment.

In particular, we offer the PHRINGE pipeline, a tool for whole genome evolutionary analysis that takes as input the complete gene set of various organisms and determines all orthologous and paralogous relationships. The output includes comparisons of intron-exon structures, multiple sequence alignments, evolutionary trees for all genes, and the relative locations of all orthologous genes mapped onto scaffolds. See an example of the application of PHRINGE to the genomes of oomycetes and diatoms. PHRINGE is part of our GATOR genome analysis and presentation system currently under development.

We perform many types of studies (using capillary as well as "next generation", e.g. "Illumina / Solexa" and "Roche / 454" approaches), including:

— Sequencing whole prokaryotic and eukaryotic genomes
— Sequencing large (e.g., "BAC") clones, mitochondrial, plastid, and viral genomes
— Sequencing ESTs and full-length cDNAs
— Environmental sequencing (i.e., "metagenomics") and sequencing for SNP discovery
— Directed finishing for gap closure and quality improvement
— Sequence assembly and validation, gene annotation, function and pathway analyses
— Constructing DNA and RNA libraries, including large-insert libraries in BAC vectors
— Evolutionary analysis of genes, gene families, and genomes
— Creating maps of the relative arrangements of homologous genes in various genomes
— Designing databases and software to meet specific needs

Genome Project Solutions also provides educational and training opportunities