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Basic local alignment search tool.
- S. Altschul, W. Gish, Webb Miller, E. Myers, D. Lipman
- Biology, Medicine
- Journal of molecular biology
- 1 October 1990
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
A Greedy Algorithm for Aligning DNA Sequences
- Z. Zhang, S. Schwartz, L. Wagner, Webb Miller
- Computer Science, Medicine
- J. Comput. Biol.
- 1 February 2000
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
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 Fugu… Expand
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-typhoid… Expand
Galaxy: a platform for interactive large-scale genome analysis.
- Belinda M Giardine, C. Riemer, +10 authors Anton Nekrutenko
- Biology, Medicine
- Genome research
- 1 October 2005
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 the… Expand
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 resulting… Expand
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 regarding… Expand
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 data… Expand
Basic local alignment search tool. Journal of Molecular Biology
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 threaded… Expand