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Basic local alignment search tool.
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP)Expand
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A Greedy Algorithm for Aligning DNA Sequences
TLDR
We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data. Expand
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and FuguExpand
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Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of non-typhoidExpand
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Galaxy: a platform for interactive large-scale genome analysis.
Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines theExpand
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PipMaker--a web server for aligning two genomic DNA sequences.
PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resultingExpand
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Human-mouse alignments with BLASTZ.
The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regardingExpand
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These dataExpand
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Aligning multiple genomic sequences with the threaded blockset aligner.
We define a "threaded blockset," which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for "threaded blockset aligner") builds a threadedExpand
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