Cross-species sequence comparisons: a review of methods and available resources.

With the availability of whole-genome sequences for an increasing number of species, we are now faced with the challenge of decoding the information contained within these DNA sequences. Comparative analysis of DNA sequences from multiple species at varying evolutionary distances is a powerful approach for identifying coding and functional noncoding sequences, as well as sequences that are unique for a given organism. In this review, we outline the strategy for choosing DNA sequences from different species for comparative analyses and describe the methods used and the resources publicly available for these studies.

[1]  Wen-Hsiung Li,et al.  Mutation rates differ among regions of the mammalian genome , 1989, Nature.

[2]  Wei Zhu,et al.  Evolutionary Strategies for the Elucidation ofcisandtransFactors That Regulate the Developmental Switching Programs of the β-like Globin Genes , 1996 .

[3]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[4]  W Miller,et al.  Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. , 1997, Gene.

[5]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[6]  Victor V. Solovyev,et al.  The Gene-Finder Computer Tools for Analysis of Human and Model Organisms Genome Sequences , 1997, ISMB.

[7]  D Haussler,et al.  Integrating database homology in a probabilistic gene structure model. , 1997, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[8]  G. Rubin,et al.  A computer program for aligning a cDNA sequence with a genomic DNA sequence. , 1998, Genome research.

[9]  W. Miller,et al.  Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. , 1999, Nucleic acids research.

[10]  Jill P. Mesirov,et al.  Human and mouse gene structure: comparative analysis and application to exon prediction , 2000, RECOMB '00.

[11]  Lior Pachter,et al.  VISTA : visualizing global DNA sequence alignments of arbitrary length , 2000, Bioinform..

[12]  R. Gibbs,et al.  PipMaker--a web server for aligning two genomic DNA sequences. , 2000, Genome research.

[13]  W Miller,et al.  Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. , 2000, Nucleic acids research.

[14]  W. J. Kent,et al.  Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. , 2000, Genome research.

[15]  E. Green,et al.  Comparative genome mapping in the sequence-based era: early experience with human chromosome 7. , 2000, Genome research.

[16]  I-Min A. Dubchak,et al.  Active conservation of noncoding sequences revealed by three-way species comparisons. , 2000, Genome research.

[17]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[18]  S. P. Fodor,et al.  Evolutionarily conserved sequences on human chromosome 21. , 2001, Genome research.

[19]  Evan E. Eichler,et al.  Positive selection of a gene family during the emergence of humans and African apes , 2001, Nature.

[20]  E. Green,et al.  Mutational and functional analyses reveal that ST7 is a highly conserved tumor-suppressor gene on human chromosome 7q31 , 2001, Nature Genetics.

[21]  Donna R. Maglott,et al.  RefSeq and LocusLink: NCBI gene-centered resources , 2001, Nucleic Acids Res..

[22]  Parvaneh Saeedi,et al.  A physical map of the mouse genome , 2002, Nature.

[23]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[24]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[25]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[26]  Jia Li,et al.  Significance Of inter-species matches when evolutionary rate varies , 2002, RECOMB '02.

[27]  Francesca Chiaromonte,et al.  Scoring Pairwise Genomic Sequence Alignments , 2001, Pacific Symposium on Biocomputing.

[28]  Paramvir S. Dehal,et al.  Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes , 2002, Science.

[29]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: 2002 update , 2002, Nucleic Acids Res..

[30]  L. Pachter,et al.  rVista for comparative sequence-based discovery of functional transcription factor binding sites. , 2002, Genome research.

[31]  William H. Majoros,et al.  A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome , 2002, Science.

[32]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[33]  L. Pachter,et al.  Strategies and tools for whole-genome alignments. , 2002, Genome research.

[34]  Jia Li,et al.  Significance of Interspecies Matches when Evolutionary Rate Varies , 2003, J. Comput. Biol..

[35]  Nicholas L. Bray,et al.  AVID: A global alignment program. , 2003, Genome research.

[36]  D. Haussler,et al.  Human-mouse alignments with BLASTZ. , 2003, Genome research.

[37]  Webb Miller,et al.  PipMaker: A World Wide Web Server for Genomic Sequence Alignments , 2003, Current protocols in bioinformatics.

[38]  D. Cox,et al.  Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. , 2003, Genome research.

[39]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.