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PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences
Laura Elnitski1, Cathy Riemer, Hanna Petrykowska
1Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA. elnitski@bio.cse.psu.edu
Genomics
|December 31, 2002
Summary
This study introduces PipTools and PipMaker, software for annotating genes and regulatory elements in genomic sequence alignments. These tools aid in identifying conserved noncoding DNA sequences, enhancing comparative genomics research.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Interspecies genomic sequence alignment is crucial for gene and regulatory element identification.
- Current alignment utility is limited by the need for extensive annotation.
- Comparative genomics requires robust tools for interpreting sequence alignments.
Purpose of the Study:
- To develop and present a suite of software tools (PipTools) and a server (PipMaker) for annotating pairwise genomic alignments.
- To facilitate the identification of functional noncoding segments and coding regions.
- To improve the interpretation of interspecies sequence comparisons.
Main Methods:
- Development of PipTools for gene and regulatory element annotation.
- Integration of PipTools with the PipMaker alignment server.
- Portable software format for common desktop use.
- Application to pairwise alignment of mouse and human MHC regions.
Main Results:
- PipTools and PipMaker provide detailed annotation for pairwise genomic alignments.
- The toolkit successfully annotated mouse and human MHC regions.
- Identified conserved, noncoding sequences with functional significance (DNase I hypersensitive sites).
Conclusions:
- PipTools and PipMaker significantly enhance the utility of interspecies genomic alignments.
- The software aids in discovering functional noncoding elements.
- This approach advances comparative genomics and the study of regulatory elements.