PipTools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences

Laura Elnitski, Cathy Riemer, Hanna Petrykowska, Liliana D Florea, Scott Schwartz, Webb Miller, Ross Hardison

Research output: Contribution to journalArticle

Abstract

Sequence conservation between species is useful both for locating coding regions of genes and for identifying functional noncoding segments. Hence interspecies alignment of genomic sequences is an important computational technique. However, its utility is limited without extensive annotation. We describe a suite of software tools, PipTools, and related programs that facilitate the annotation of genes and putative regulatory elements in pairwise alignments. The alignment server PipMaker uses the output of these tools to display detailed information needed to interpret alignments. These programs are provided in a portable format for use on common desktop computers and both the toolkit and the PipMaker server can be found at our Web site (http://bio.cse.psu.edu/). We illustrate the utility of the toolkit using annotation of a pairwise comparison of the mouse MHC class II and class III regions with orthologous human sequences and subsequently identify conserved, noncoding sequences that are DNase I hypersensitive sites in chromatin of mouse cells.

Original languageEnglish (US)
Pages (from-to)681-690
Number of pages10
JournalGenomics
Volume80
Issue number6
DOIs
StatePublished - 2002
Externally publishedYes

Fingerprint

Data Display
Molecular Sequence Annotation
Conserved Sequence
Sequence Alignment
Deoxyribonuclease I
Regulator Genes
Chromatin
Software
Genes

Keywords

  • Computational biology
  • DNA
  • Sequence alignment
  • Sequence analysis

ASJC Scopus subject areas

  • Genetics

Cite this

Elnitski, L., Riemer, C., Petrykowska, H., Florea, L. D., Schwartz, S., Miller, W., & Hardison, R. (2002). PipTools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics, 80(6), 681-690. https://doi.org/10.1006/geno.2002.7018

PipTools : A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. / Elnitski, Laura; Riemer, Cathy; Petrykowska, Hanna; Florea, Liliana D; Schwartz, Scott; Miller, Webb; Hardison, Ross.

In: Genomics, Vol. 80, No. 6, 2002, p. 681-690.

Research output: Contribution to journalArticle

Elnitski, L, Riemer, C, Petrykowska, H, Florea, LD, Schwartz, S, Miller, W & Hardison, R 2002, 'PipTools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences', Genomics, vol. 80, no. 6, pp. 681-690. https://doi.org/10.1006/geno.2002.7018
Elnitski, Laura ; Riemer, Cathy ; Petrykowska, Hanna ; Florea, Liliana D ; Schwartz, Scott ; Miller, Webb ; Hardison, Ross. / PipTools : A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. In: Genomics. 2002 ; Vol. 80, No. 6. pp. 681-690.
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