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Titolo:
PipMaker - A Web server for aligning two genomic DNA sequences
Autore:
Schwartz, S; Zhang, Z; Frazer, KA; Smit, A; Riemer, C; Bouck, J; Gibbs, R; Hardison, R; Miller, W;
Indirizzi:
Penn State Univ, Dept Comp Sci & Engn, University Pk, PA 16802 USA Penn State Univ University Pk PA USA 16802 n, University Pk, PA 16802 USA Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA PennState Univ University Pk PA USA 16802 l, University Pk, PA 16802 USA Penn State Univ, Ctr Gene Regulat, University Pk, PA 16802 USA Penn State Univ University Pk PA USA 16802 t, University Pk, PA 16802 USA Univ Calif Berkeley, Lawrence Berkeley Lab, Genome Sci Dept, Berkeley, CA 94720 USA Univ Calif Berkeley Berkeley CA USA 94720 ci Dept, Berkeley, CA 94720 USA Axys Pharmaceut, La Jolla, CA 92037 USA Axys Pharmaceut La Jolla CA USA 92037 Pharmaceut, La Jolla, CA 92037 USA Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA Baylor CollMed Houston TX USA 77030 & Human Genet, Houston, TX 77030 USA
Titolo Testata:
GENOME RESEARCH
fascicolo: 4, volume: 10, anno: 2000,
pagine: 577 - 586
SICI:
1088-9051(200004)10:4<577:P-AWSF>2.0.ZU;2-U
Fonte:
ISI
Lingua:
ENG
Soggetto:
ESCHERICHIA-COLI K-12; SALMONELLA-TYPHIMURIUM; GENE; EVOLUTION; REGION; FLAVOHEMOGLOBIN; IDENTIFICATION; GENERATION; DATABASE; PROGRAMS;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
39
Recensione:
Indirizzi per estratti:
Indirizzo: Miller, W Penn State Univ, Dept Comp Sci & Engn, University Pk, PA 16802 USA Penn State Univ University Pk PA USA 16802 ity Pk, PA 16802 USA
Citazione:
S. Schwartz et al., "PipMaker - A Web server for aligning two genomic DNA sequences", GENOME RES, 10(4), 2000, pp. 577-586

Abstract

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 alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree of similarity for each aligning segment between the twosequences in a compact and easily understandable form. Positions along thehorizontal axis can be labeled with features such as exons of genes and repetitive elements, and colors can be used to clarify and enhance the display. The web site also provides a plot of the Locations of those segments in both species (similar to a dot plot). PipMaker is appropriate for comparinggenomic sequences from any two related species, although the types of information that can be inferred (e.g., protein-coding regions and cis-regulatory elements) depend on the level of conservation and the time and divergence rate since the separation of the species. Gene regulatory elements are often detectable as similar, noncoding sequences in species that diverged as much as 100-300 million years ago, such as humans and mice, Caenorhabditis elegans and C. briggsae, or Escherichia coli and Salmonella spp. PipMaker supports analysis of unfinished or "working draft" sequences by permitting one of the two sequences to be in unoriented and unordered contigs.

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Documento generato il 07/07/20 alle ore 15:38:52