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

Genomics

Volumn 80, Issue 6, 2002, Pages 681-690

  Elnitski, Laura ^a,c   Riemer, Cathy ^a   Petrykowska, Hanna ^a   Florea, Liliana ^b   Schwartz, Scott ^a   Miller, Webb ^a,c   Hardison, Ross ^a  

^a Department of Computer Science ^*  (United States)

^b CELERA GENOMICS   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Computational biology; DNA; Sequence alignment; Sequence analysis

Indexed keywords

CONTIG; DEOXYRIBONUCLEASE I; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 3;

ARTICLE; BINDING SITE; CALCULATION; CHROMATIN STRUCTURE; COMPUTER PROGRAM; GENE SEQUENCE; GENOMICS; INTERNET; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

EID: 0036935568     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.2002.7018     Document Type: Article

References (20)

1. Fortna, A., and Gardiner, K. (2001). Genomic sequence analysis tools: A user's guide. Trends Genet. 17: 158-164.
2. Makalowski, W., Zhang, J., and Boguski, M. S. (1996). Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res. 6: 846-857.
3. Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B., and Lander, E. S. (2000). Human and mouse gene structure: Comparative analysis and application to exon prediction. Genome Res. 10: 950-958.
4. Loots, G. G., et al. (2000). Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288: 136-140.
5. Mallon, A. M., et al. (2000). Comparative genome sequence analysis of the Bpa/Str region in mouse and man. Genome Res. 10: 758-775.
6. Hardison, R. C. (2000). Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16: 369-372.
7. Schwartz, S., et al. (2000). PipMaker-A Web server for aligning two genomic DNA sequences. Genome Res. 10: 577-586.
8. Mayor, C., et al. (2000). VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16: 1046-1047.
9. Burge, C., and Karlin, S. (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
10. Florea, L., Hartzell, G., Zhang, Z., Rubin, G. M., and Miller, W. (1998). A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8: 967-974.
11. Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. (2000). A greedy algorithm for aligning DNA sequences. J. Comp. Biol. 7: 203-214.
12. Elnitski, L., Riemer, C., Schwartz, S., Hardison, R., and Miller, W. (2002). PipMaker: A World Wide Web server for genomic sequence alignments. Curr. Protocols (in press).
13. Wilson, M. D., et al. (2001). Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. Nucleic Acids Res. 29: 1352-1365.
14. Gardiner-Garden, M., and Frommer, M. (1987). CpG islands in vertebrate genomes. J. Mol. Biol. 196: 261-282.
15. Zhang, M. Q. (1997). Identification of protein coding regions in the human genome based on quadratic discriminant analysis. Proc. Natl. Acad. Sci. USA 94: 565-568.
16. Gross, D. S., and Garrard, W. T. (1988). Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57: 159-197.
17. Lovering, R., et al. (1993). Identification and preliminary characterization of a protein motif related to the zinc finger. Proc. Natl. Acad. Sci. USA 90: 2112-2116.
18. Friend, C., Scher, W., Holland, J. G., and Sato, T. (1971). Hemoglobin synthesis in murine virus-induced leukemic cells in vitro: Stimulation of erythroid differentiation by dimethyl sulfoxide. Proc. Natl. Acad. Sci. USA 68: 378-382.
19. Dhar, V., Nandi, A., Schildkraut, C. L., and Skoultchi, A. I. (1990). Erythroid-specific nuclease-hypersensitive sites flanking the human beta-globin domain. Mol. Cell. Biol. 10: 4324-4333.
20. Molete, J. M., Petrykowska, H., Sigg, M., Miller, W., and Hardison, R. (2002). Functional and binding studies of HS3.2 of the beta-globin locus control region. Gene 283: 185-197.