PipMaker--a web server for aligning two genomic DNA sequences.

By Scott Schwartz, Zheng Zhang, Kelly A. Frazer, Arian F. A. Smit, C. Riemer, J. Bouck, Richard A. Gibbs, Ross C. Hardison, W. Miller. Genome Research, 2000

1,263 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/377fc5473794c2a62dc31f2260d8834459be7938

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In Molecular Biology

1. David Haussler
2. W. James Kent
3. Steven L. Salzberg
4. Robert S. Harris
5. Lior S. Pachter
6. Gabriela G. Loots
7. Ivan Ovcharenko
8. Adam C. Siepel

Citations in the corpus

• Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence (2003, background): “There are Web sites that provide these services, e.g., PipMaker ( UNIT 10.2; Schwartz et al., 2000) or rVista (Loots et al., 2002).”
• Poxvirus Orthologous Clusters: toward Defining the Minimum Essential Poxvirus Genome (2003, background): “POCs for viewing Dotter results [54]), Laj (local alignment in JAVA [46]), and”
• Transcriptional regulation by calcium, calcineurin, and NFAT. (2003, background): “These regions often (but not always) correspond to highly conserved noncoding sequences (CNS) identified by comparing the sequences of gene loci in two or more mammalian genomes using Web-based programs such as VISTA (Mayor et al. 2000; Loots et al. 2002; Bray et al. 2003) or PipMaker (Schwartz et a”
• Aligning multiple genomic sequences with the threaded blockset aligner. (2004, background): “Extensions of TBA to automatically produce the richer class of blocksets obtained by dropping these requirements remain as future work.”
• Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12 (2005, methodology): “PipMaker was used to obtain a percent identity plot of the alignment of genomic regions of rice and sorghum (Schwartz et al. 2000).”
• Human-mouse alignments with BLASTZ. (2003, methodology): “Preliminary studies indicated that an appropriate level of sensitivity and specificity was attained by a program called BLASTZ, which is used by the PipMaker webserver (Schwartz et al. 2000) to align genomic sequences.”
• Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing (2015, methodology): “In addition, we performed reciprocal BLASTZ searches [114] between two species in syntenic regions and identified clear orthologs based on E-values (cut-off: 1e) and phylogenetic analyses.”
• rVista for comparative sequence-based discovery of functional transcription factor binding sites. (2002, methodology): “The computational algorithms developed to perform comparative sequence analysis are based either on local alignments ( BLAST Altschul et al. 1990]; PIPMaker [Schwartz et al. 2000]) or on global alignments ( AVID ; VISTA [Mayor et al., 2000;])”
• Alignment-free sequence comparison: benefits, applications, and tools (2017, background): “Therefore, despite the wealth of tools and more than 15 years of research [7, 21 – 25], the problem of long sequence alignment is not fully resolved [26].”
• VISTA : visualizing global DNA sequence alignments of arbitrary length (2000, methodology): “For longer alignments, the only widely available visualization tool is PIPMaker (Schwartz et al., 2000).”
• ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes (2004, methodology): “The conservation-profile visualization scheme of the ECR Browser tool is based on an idea originally implemented in the PipMaker tool (21) and later adopted by both Vista (22) and zPicture (23).”
• Current methods of gene prediction, their strengths and weaknesses. (2002, background): “Finally, several programs try to retrieve information on conservation or synteny between organisms from genomic alignments, as, for example, MUMmer (76), WABA (77), PipMaker (78) and DIALIGN (79).”
• Improved pairwise alignment of genomic dna (2007, methodology): “Initially designed as a piece of the PipMaker server (Schwartz et al. 2000), it has received widespread use in the scientific community, serving, for example, as the first stage in generating whole genome alignments for the UCSC Genome Browser (http://genome.ucsc.edu).”