Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

MELT - a Translated Domain Specific Language Embedded in the GCC Compiler

The GCC free compiler is a very large software, compiling source in several languages for many targets on various systems. It can be extended by plugins, which may take advantage of its power to provide extra specific functionality (warnings, optimizations, source refactoring or navigation) by processing various GCC internal representations (Gimple, Tree, ...). Writing plugins in C is a complex and time-consuming task, but customizing GCC by using an existing scripting language inside is impractical. We describe MELT, a specific Lisp-like DSL which fits well into existing GCC technology and offers high-level features (functional, object or reflexive programming, pattern matching). MELT is translated to C fitted for GCC internals and provides various features to facilitate this. This work shows that even huge, legacy, software can be a posteriori extended by specifically tailored and translated high-level DSLs.Comment: In Proceedings DSL 2011, arXiv:1109.032