An Improved Tool for Molecular Biology

Abstract

I n 1998, Oxford Molecular Group released a comprehensive nucleic acid and protein sequence analysis package for the Windows platform. This package provided a significant resource for investigators who wished to have sequence analysis capabilities on their own PC. In its latest release, OMIGA 2.0, a number of new features have been included along with several fixes and improvements. The program runs under Windows 95, 98, or NT, and it represents a powerful tool for molecular biology. The application requires about 50 MB of disk space and runs well on a Pentium II machine with 32 MB of memory. Some sequence database searches require an Internet connection, through either modem or network. All of the features of the first release of the program are retained; added are several capabilities to enhance both nucleic acid and protein sequences. The 2.0 version is provided on a single CD ROM, which also contains updated versions of databases for protein motifs (PROSITE), restriction enzyme sites (REBASE), protein cleavage sites (PABASE), and nucleic acid motifs (NASITE). RasMol 2.6 is included to facilitate visualization of data from Protein Data Bank (PDB) files. A database of sequences for use in OMIGA, Vecbank, is also provided. This software can perform sequence composition analysis; search sequences for digestion sites, coding regions, and specific sequence motifs. It contains functions useful for using the polymerase chain reaction, such as identifying primer pairs, predicting primer properties, and also identifying DNA sequencing primers. Algorithms for identifying sequence similarity include BLAST searches of the National Center for Biotechnology Information (NCBI) and Entrez databases; multiple alignments (protein and nucleic acid sequences); and dot plot alignments. OMIGA 2 also contains numerous modules for protein analysis, including prediction of protein secondary structure; calculation of hydropathy and antigenicity profiles; translation; and reverse translation. This release contains an enhanced ability to utilize BLAST algorithms to compare local sequences with the NCBI database; increased flexibility in searching and retrieving sequences from the NCBI and Entrez databases; and a new feature for sequence comparison display as dot plots. In addition, an increased capacity to search for and evaluate primers, including your own test primers in a selected sequence, is provided. New protein analysis features include an option to calculate the isoelectric point and the charge of a peptide sequence at neutral pH and an enhanced display of secondary structural features in a variety of sequence views. Consensus cutoff value selection is now available in both DNA and protein sequence comparisons. A flexible user selection of display color schemes has also been added. User friendliness has been improved with a startup dialog box, which allows the user to select a new project, work on an already existing project in OMIGA, or open a project from a location outside the OMIGA folder or directory. The program retains the File Manager/Windows Explorer format for file and project organization. A simple command for recalculations is provided for searches, which can be edited and then recalculated on the fly. Printing formats have been improved as well to address problems in previous versions of the program. The file import capability has been enhanced. The zoom command in the features view now allows a user to enlarge sequence regions so that individual bases can be seen on screen. Another program enhancement allows the user to move between consecutive features at the residue level in the map view. The excellent documentation and online help provided with OMIGA 1.1 has been retained and further improved. Although some problems with the earlier release of OMIGA have been addressed in this new version, several still remain. These include alerting the user erroneously with messages of file attribute problems when limited free space remains on the hard drive, requiring the user to delete file types manually from a temp folder, requiring files to be deleted files from within the program to avoid corruption of projects, and limiting the number of files that can be selected within some modes. Some problems also remain with outputting maps to Windows metafiles. The publisher provides work-arounds for most of these problems, and they represent only minor inconveniences when run on a PC with sufficient disk space. This release of OMIGA improves the software product, which should continue to serve as a valuable resource to laboratories that require rapid sequence analyses and definition of strategies for such procedures as cloning and PCR primer design, as well as analysis of peptide and protein sequence properties. OMIGA 2.0 Genetics Computer Group, an Oxford Molecular Company Madison, WI. $1995 commercial, $1495 academic/government. 800-876-9994