Big Data with SQLite

Posted Posted in bioinformatics, database, genome informatics

I recently wanted to process genome-wide sequence data that I had extracted into 24 files ranging in size from 3 GB (Gigabytes) for the small chromosome Y to 26 GB for the largest chromosome 1. Further processing this data was challenging as any software script reading the files has to do it in a stream, […]

Telomeric Regions of the Human Genome

Posted Posted in genome informatics, genomics

Telomeres form caps on the ends of chromosomes that prevent fusion of chromosomal ends and provide genomic stability. During gametogenesis, reprogramming of the germ cells leads to elongation of telomeres up to their species-specific maximum. In normal somatic cells, telomeres are progressively shortened with every cell division. This shortening in normal human cells limits the number of […]

Microdeletion and Microduplication Syndromes in the Human Genome

Posted Posted in genome informatics, genomics, health

Small changes in the sequence of human chromosomes can have detrimental effects in the person’s health and development. The often affect multiple genes but are too small to be visible with traditional karyotyping methods. These changes seem to appear near regions of low complexity (repetitive sequence regions) with some consistency as novel mutations. The following […]