Paircomp, FamilyRelationsII and Cartwheel: Tools for interspecific sequence comparison

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Brown, C Titus ^a   Xie, Yuan ^a   Davidson, Eric H ^a   Cameron, R Andrew ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL GENOMES; COMPARATIVE ANALYSIS; COMPARATIVE SEQUENCE ANALYSIS; GENOMIC REGIONS; INTERACTIVE EXPLORATION; MANAGEMENT SYSTEMS; REGULATORY REGIONS; SEQUENCE COMPARISONS;

ANIMALS; GENES;

TOOLS;

COMPLEMENTARY DNA;

ALGORITHM; ANIMAL GENETICS; ARTICLE; BIOINFORMATICS; ECHINODERM; GENE SEQUENCE; GENOMICS; INTERNET; MAMMAL; NEMATODE; NONHUMAN; REGULATOR GENE; SEQUENCE ANALYSIS; ANIMAL; BACTERIAL ARTIFICIAL CHROMOSOME; BIOLOGY; CLUSTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA SEQUENCE; EXON; GENETIC DATABASE; GENOME; HUMAN; HUMAN GENOME; METABOLISM; MOLECULAR GENETICS; MOUSE; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; PROCEDURES; PROMOTER REGION; REGULATORY SEQUENCE; SEQUENCE ALIGNMENT;

ANIMALIA; ECHINODERMATA; MAMMALIA; NEMATODA;

ALGORITHMS; ANIMALS; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; EXONS; GENES, REGULATOR; GENOME; GENOME, HUMAN; GENOMICS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 25444500431     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-70     Document Type: Article

References (22)

1. Cooper GM, Sidow A: Genomic regulatory regions: insights from comparative sequence analysis. Curr Opin Genet Dev 2003, 13(6):604-610.
2. Brown CT, Rust AG, Clarke PJ, Pan Z, Schilstra MJ, De Buysscher T, Griffin G, Wold BJ, Cameron RA, Davidson EH, Bolouri H: New computational approaches for analysis of cis-regulatory networks. Dev Biol 2002, 246(1):86-102.
3. Yuh CH, Brown CT, Livi CB, Rowen L, Clarke PJ, Davidson EH: Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev Biol 2002, 246(1):148-161.
4. Kirouac M, Sternberg PW: 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.
5. Romano LA, Wray GA: Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development 2003, 130(17):4187-4199.
6. Leung TH, Hoffmann A, Baltimore D: One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers. Cell 2004, 118(4):453-464.
7. Revilla-i-Domingo R, Minokawa T, Davidson EH: 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):438-451.
8. PyZine online magazine [http://www.pyzine.com/Issue006/index.html]
9. FamilyRelations Web site [http://family.caltech.edu/]
10. Caltech Cartwheel server, "Woodward" [http://woodward.caltech.edu/canal/]
11. FamilyRelations tutorial [http://family.caltech.edu/tutorial/]
12. Sonnhammer EL, 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.
13. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
14. Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res 2003, 13(1):97-102.
15. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003, 13(4):721-731.
16. Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R: PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics 2002, 80(6):681-690.
17. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W: PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 2000, 10(4):577-586.
18. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32(Web Server):W273-279.
19. Yi TM, 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):3027-3033.
20. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268(1):78-94.
21. Parra G, Blanco E, Guigo R: GeneID in Drosophila. Genome Res 2000, 10(4):511-515.
22. Krogh A: Using database matches with for HMMGene for automated gene detection in Drosophila. Genome Res 2000, 10(4):523-528.