MICA: desktop software for comprehensive searching of DNA databases

BACKGROUND: Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. RESULTS: MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. CONCLUSION: MICA is suitable as a search engine for desktop DNA analysis software

Impact of central nervous system-directed treatment on competence and adjustment among children in early cancer survivorship

Background: Central nervous system (CNS)-directed treatments can cause long-term academic, social, and emotional difficulties for children with cancer. However, limited research has examined the emergence of problems longitudinally and has often stratified risk by diagnosis alone. Therefore, this study compared competence and adjustment in children, who did and did not receive CNS-directed treatment, over the first 3 years following a cancer diagnosis. Procedure: Mothers, fathers, and children (ages 5–18 years at diagnosis) from 217 families reported on the child's competence (academic, social) and adjustment (anxious/depressed, withdrawn/depressed) near a new cancer diagnosis or relapse and 3 years later. Children were categorized into CNS-directed treatment (n = 112; including cranial radiation, intrathecal chemotherapy, and/or neurosurgery) and non-CNS-directed treatment (n = 105) groups. Results: At enrollment, there were few differences in competence and emotional adjustment among children based on treatment or diagnostic group. At 3 years, mothers and fathers reported poorer social competence for the CNS-directed treatment group, and fathers reported poorer school competence for the CNS-directed treatment group. Over time, father ratings of social competence increased for the non-CNS-directed treatment group, but not the CNS-directed treatment group. While father ratings of academic competence declined for the CNS-directed treatment group, mother ratings declined the most for children diagnosed with a brain tumor. All children demonstrated higher anxious/depressed scores over time. Conclusions: CNS-directed treatment may be a valuable indicator to identify childhood cancer survivors at risk for poor competence during early survivorship. Follow-up screening and supportive services are recommended, as well as additional longitudinal research