Dynamic Decompression for Text Files

Compression algorithms reduce the redundancy in data representation to decrease the storage required for that data. Lossless compression researchers have developed highly sophisticated approaches, such as Huffman encoding, arithmetic encoding, the Lempel-Ziv (LZ) family, Dynamic Markov Compression (DMC), Prediction by Partial Matching (PPM), and Burrows-Wheeler Transform (BWT) based algorithms. Decompression is also required to retrieve the original data by lossless means. A compression scheme for text files coupled with the principle of dynamic decompression, which decompresses only the section of the compressed text file required by the user instead of decompressing the entire text file. Dynamic decompressed files offer better disk space utilization due to higher compression ratios compared to most of the currently available text file formats.

Finding Approximate Tandem Repeats with the Burrows-Wheeler Transform

Approximate tandem repeats in a genomic sequence are two or more contiguous, similar copies of a pattern of nucleotides. They are used in DNA mapping, studying molecular evolution mechanisms, forensic analysis and research in diagnosis of inherited diseases. All their functions are still investigated and not well defined, but increasing biological databases together with tools for identification of these repeats may lead to discovery of their specific role or correlation with particular features. This paper presents a new approach for finding approximate tandem repeats in a given sequence, where the similarity between consecutive repeats is measured using the Hamming distance. It is an enhancement of a method for finding exact tandem repeats in DNA sequences based on the Burrows- Wheeler transform.