Paircomp, FamilyRelationsII and Cartwheel: Tools for Interspecific Sequence Comparison

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2005 Mar 26

PMID 15790396

Citations 20

Authors

C Titus Brown

Yuan Xie

Eric H Davidson

R Andrew Cameron

Affiliations

Soon will be listed here.

Abstract

Background: Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes.

Results: We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at http://family.caltech.edu/.

Conclusion: These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.

Citing Articles

Transcription of microRNAs is regulated by developmental signaling pathways and transcription factors.

Arnott M, Sampilo N, Song J Front Cell Dev Biol. 2024; 12:1356589.

PMID: 38721525 PMC: 11076791. DOI: 10.3389/fcell.2024.1356589.

Do echinoderm genomes measure up?.

Cameron R, Kudtarkar P, Gordon S, Worley K, Gibbs R Mar Genomics. 2015; 22:1-9.

PMID: 25701080 PMC: 4489978. DOI: 10.1016/j.margen.2015.02.004.

Cis-regulatory control of the nuclear receptor Coup-TF gene in the sea urchin Paracentrotus lividus embryo.

Kalampoki L, Flytzanis C PLoS One. 2014; 9(11):e109274.

PMID: 25386650 PMC: 4227642. DOI: 10.1371/journal.pone.0109274.

Developmental cis-regulatory analysis of the cyclin D gene in the sea urchin Strongylocentrotus purpuratus.

McCarty C, Coffman J Biochem Biophys Res Commun. 2013; 440(3):413-8.

PMID: 24090975 PMC: 3871186. DOI: 10.1016/j.bbrc.2013.09.094.

Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis.

Ransick A, Davidson E Dev Biol. 2012; 364(2):259-67.

PMID: 22509525 PMC: 3561781. DOI: 10.1016/j.ydbio.2012.02.003.

References

Parra G, Blanco E, Guigo R . GeneID in Drosophila. Genome Res. 2000; 10(4):511-5. PMC: 310871. DOI: 10.1101/gr.10.4.511. View

Burge C, Karlin S . Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997; 268(1):78-94. DOI: 10.1006/jmbi.1997.0951. View

Schwartz S, Zhang Z, Frazer K, Smit A, Riemer C, Bouck J . PipMaker--a web server for aligning two genomic DNA sequences. Genome Res. 2000; 10(4):577-86. PMC: 310868. DOI: 10.1101/gr.10.4.577. View

Brown C, Rust A, Clarke P, Pan Z, Schilstra M, De Buysscher T . New computational approaches for analysis of cis-regulatory networks. Dev Biol. 2002; 246(1):86-102. DOI: 10.1006/dbio.2002.0619. View

Yuh C, Brown C, Livi C, Rowen L, Clarke P, Davidson E . Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev Biol. 2002; 246(1):148-61. DOI: 10.1006/dbio.2002.0618. View

Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W . PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics. 2002; 80(6):681-90. DOI: 10.1006/geno.2002.7018. View

Bray N, Dubchak I, Pachter L . AVID: A global alignment program. Genome Res. 2003; 13(1):97-102. PMC: 430967. DOI: 10.1101/gr.789803. View

Brudno M, Do C, Cooper G, Kim M, Davydov E, Green E . LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003; 13(4):721-31. PMC: 430158. DOI: 10.1101/gr.926603. View

Kirouac M, Sternberg P . cis-Regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae. Dev Biol. 2003; 257(1):85-103. DOI: 10.1016/s0012-1606(03)00032-0. View

10.

Romano L, Wray G . Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development. 2003; 130(17):4187-99. DOI: 10.1242/dev.00611. View

11.

Cooper G, Sidow A . Genomic regulatory regions: insights from comparative sequence analysis. Curr Opin Genet Dev. 2003; 13(6):604-10. DOI: 10.1016/j.gde.2003.10.001. View

12.

Frazer K, Pachter L, Poliakov A, Rubin E, Dubchak I . VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004; 32(Web Server issue):W273-9. PMC: 441596. DOI: 10.1093/nar/gkh458. View

13.

Leung T, Hoffmann A, Baltimore D . One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell. 2004; 118(4):453-64. DOI: 10.1016/j.cell.2004.08.007. View

14.

Revilla-I-Domingo R, Minokawa T, Davidson E . R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres. Dev Biol. 2004; 274(2):438-51. DOI: 10.1016/j.ydbio.2004.07.008. View

15.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

16.

Yi T, Walsh K, Schimmel P . Rabbit muscle creatine kinase: genomic cloning, sequencing, and analysis of upstream sequences important for expression in myocytes. Nucleic Acids Res. 1991; 19(11):3027-33. PMC: 328266. DOI: 10.1093/nar/19.11.3027. View

17.

Sonnhammer E, Durbin R . A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene. 1995; 167(1-2):GC1-10. DOI: 10.1016/0378-1119(95)00714-8. View

18.

KROGH A . Using database matches with for HMMGene for automated gene detection in Drosophila. Genome Res. 2000; 10(4):523-8. PMC: 310864. DOI: 10.1101/gr.10.4.523. View