Kraken: ultrafast metagenomic sequence classification using exact alignments

Ultrafast clustering algorithms for metagenomic sequence analysis

The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence d...

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Metagenomic sequence classification is a procedure to assign sequences to their source genomes. It is one of the important steps for metagenomic sequence data analysis. Although many methods exist, classification of high-throughput metagenomic sequence data in a limited time is still a challenge. We present here an ultra-fast metagenomic sequence classification system (MetaBinG) using graphic p...

Malware Similarity Analysis using API Sequence Alignments

Malware variants could be defined as malware that have similar malcious behavior. In this paper, a sequence alignment method, the method widely used in Bioinformatics, was used to detect malware variants. This method can find the common parts of Malware’s API call sequences, and these common API call sequences can be used to detect similar behaviors of malware variants. However, when a sequence...

Sequence Database Search Using Jumping Alignments

We describe a new algorithm for amino acid sequence classification and the detection of remote homologues. The rationale is to exploit both vertical and horizontal information of a multiple alignment in a well balanced manner. This is in contrast to established methods like profiles and hidden Markov models which focus on vertical information as they model the columns of the alignment independe...

Assessing Multiple Sequence Alignments Using Visual Tools