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The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and… Expand As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used… Expand Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental… Expand The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA… Expand Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human… Expand Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based… Expand The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original… Expand Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and… Expand We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its… Expand An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of… Expand