Benchmarking tools for the alignment of functional noncoding DNA
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004)
BMC Bioinformatics 5(1): 6.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Pollard, Daniel A.;
Bergman, Casey M.;
Stoye, JensUniBi ;
Celniker, Susan E.;
Eisen, Michael B.
Einrichtung
Abstract / Bemerkung
Background: Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of protein-coding sequences typically have been benchmarked against "correct" alignments inferred from structural data. For noncoding sequences, where such independent validation is lacking, simulation provides an effective means to generate "correct" alignments with which to benchmark alignment tools. Results: Using rates of noncoding sequence evolution estimated from the genus Drosophila, we simulated alignments over a range of divergence times under varying models incorporating point substitution, insertion/deletion events, and short blocks of constrained sequences such as those found in cis-regulatory regions. We then compared "correct" alignments generated by a modified version of the ROSE simulation platform to alignments of the simulated derived sequences produced by eight pairwise alignment tools (Avid, BlastZ, Chaos, ClustalW, DiAlign, Lagan, Needle, and WABA) to determine the off-the-shelf performance of each tool. As expected, the ability to align noncoding sequences accurately decreases with increasing divergence for all tools, and declines faster in the presence of insertion/deletion evolution. Global alignment tools (Avid, ClustalW, Lagan, and Needle) typically have higher sensitivity over entire noncoding sequences as well as in constrained sequences. Local tools (BlastZ, Chaos, and WABA) have lower overall sensitivity as a consequence of incomplete coverage, but have high specificity to detect constrained sequences as well as high sensitivity within the subset of sequences they align. Tools such as DiAlign, which generate both local and global outputs, produce alignments of constrained sequences with both high sensitivity and specificity for divergence distances in the range of 1.25 - 3.0 substitutions per site. Conclusion: For species with genomic properties similar to Drosophila, we conclude that a single pair of optimally diverged species analyzed with a high performance alignment tool can yield accurate and specific alignments of functionally constrained noncoding sequences. Further algorithm development, optimization of alignment parameters, and benchmarking studies will be necessary to extract the maximal biological information from alignments of functional noncoding DNA.
Erscheinungsjahr
2004
Zeitschriftentitel
BMC Bioinformatics
Band
5
Ausgabe
1
Art.-Nr.
6
ISSN
1471-2105
Page URI
https://pub.uni-bielefeld.de/record/1773312
Zitieren
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics. 2004;5(1): 6.
Pollard, D. A., Bergman, C. M., Stoye, J., Celniker, S. E., & Eisen, M. B. (2004). Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics, 5(1), 6. https://doi.org/10.1186/1471-2105-5-6
Pollard, Daniel A., Bergman, Casey M., Stoye, Jens, Celniker, Susan E., and Eisen, Michael B. 2004. “Benchmarking tools for the alignment of functional noncoding DNA”. BMC Bioinformatics 5 (1): 6.
Pollard, D. A., Bergman, C. M., Stoye, J., Celniker, S. E., and Eisen, M. B. (2004). Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5:6.
Pollard, D.A., et al., 2004. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics, 5(1): 6.
D.A. Pollard, et al., “Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, vol. 5, 2004, : 6.
Pollard, D.A., Bergman, C.M., Stoye, J., Celniker, S.E., Eisen, M.B.: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics. 5, : 6 (2004).
Pollard, Daniel A., Bergman, Casey M., Stoye, Jens, Celniker, Susan E., and Eisen, Michael B. “Benchmarking tools for the alignment of functional noncoding DNA”. BMC Bioinformatics 5.1 (2004): 6.
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Daten bereitgestellt von European Bioinformatics Institute (EBI)
71 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites.
Covington BC, McLean JA, Bachmann BO., Nat Prod Rep 34(1), 2017
PMID: 27604382
Covington BC, McLean JA, Bachmann BO., Nat Prod Rep 34(1), 2017
PMID: 27604382
The appeasement of Doug: a synthetic approach to enhancer biology.
Vincent BJ, Estrada J, DePace AH., Integr Biol (Camb) 8(4), 2016
PMID: 26936291
Vincent BJ, Estrada J, DePace AH., Integr Biol (Camb) 8(4), 2016
PMID: 26936291
Association of obesity with serum leptin, adiponectin, and serotonin and gut microflora in beagle dogs.
Park HJ, Lee SE, Kim HB, Isaacson RE, Seo KW, Song KH., J Vet Intern Med 29(1), 2015
PMID: 25407880
Park HJ, Lee SE, Kim HB, Isaacson RE, Seo KW, Song KH., J Vet Intern Med 29(1), 2015
PMID: 25407880
BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.
De Witte D, Van de Velde J, Decap D, Van Bel M, Audenaert P, Demeester P, Dhoedt B, Vandepoele K, Fostier J., Bioinformatics 31(23), 2015
PMID: 26254488
De Witte D, Van de Velde J, Decap D, Van Bel M, Audenaert P, Demeester P, Dhoedt B, Vandepoele K, Fostier J., Bioinformatics 31(23), 2015
PMID: 26254488
Methods to detect selection on noncoding DNA.
Zhen Y, Andolfatto P., Methods Mol Biol 856(), 2012
PMID: 22399458
Zhen Y, Andolfatto P., Methods Mol Biol 856(), 2012
PMID: 22399458
Use of ChIP-Seq data for the design of a multiple promoter-alignment method.
Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C., Nucleic Acids Res 40(7), 2012
PMID: 22230796
Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C., Nucleic Acids Res 40(7), 2012
PMID: 22230796
Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.
Reineke AR, Bornberg-Bauer E, Gu J., Nucleic Acids Res 39(14), 2011
PMID: 21470961
Reineke AR, Bornberg-Bauer E, Gu J., Nucleic Acids Res 39(14), 2011
PMID: 21470961
Towards realistic benchmarks for multiple alignments of non-coding sequences.
Kim J, Sinha S., BMC Bioinformatics 11(), 2010
PMID: 20102627
Kim J, Sinha S., BMC Bioinformatics 11(), 2010
PMID: 20102627
Cgaln: fast and space-efficient whole-genome alignment.
Nakato R, Gotoh O., BMC Bioinformatics 11(), 2010
PMID: 20433723
Nakato R, Gotoh O., BMC Bioinformatics 11(), 2010
PMID: 20433723
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment.
Aniba MR, Poch O, Thompson JD., Nucleic Acids Res 38(21), 2010
PMID: 20639539
Aniba MR, Poch O, Thompson JD., Nucleic Acids Res 38(21), 2010
PMID: 20639539
Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: transcriptional dynamics and regulatory structures.
Nguyen TT, Almon RR, Dubois DC, Jusko WJ, Androulakis IP., BMC Bioinformatics 11(), 2010
PMID: 20946642
Nguyen TT, Almon RR, Dubois DC, Jusko WJ, Androulakis IP., BMC Bioinformatics 11(), 2010
PMID: 20946642
A genome alignment algorithm based on compression.
Cao MD, Cao MD, Dix TI, Allison L., BMC Bioinformatics 11(), 2010
PMID: 21159205
Cao MD, Cao MD, Dix TI, Allison L., BMC Bioinformatics 11(), 2010
PMID: 21159205
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.
He X, Ling X, Sinha S., PLoS Comput Biol 5(3), 2009
PMID: 19293946
He X, Ling X, Sinha S., PLoS Comput Biol 5(3), 2009
PMID: 19293946
Comparative genomic workflow: discovery of conserved noncoding DNA patterns.
Rajapakse J, Pooja, Chen C, Ho SL., IEEE Eng Med Biol Mag 28(4), 2009
PMID: 19622420
Rajapakse J, Pooja, Chen C, Ho SL., IEEE Eng Med Biol Mag 28(4), 2009
PMID: 19622420
Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura.
Marion de Procé S, Halligan DL, Keightley PD, Charlesworth B., J Mol Evol 69(6), 2009
PMID: 19859648
Marion de Procé S, Halligan DL, Keightley PD, Charlesworth B., J Mol Evol 69(6), 2009
PMID: 19859648
Uncertainty in homology inferences: assessing and improving genomic sequence alignment.
Lunter G, Rocco A, Mimouni N, Heger A, Caldeira A, Hein J., Genome Res 18(2), 2008
PMID: 18073381
Lunter G, Rocco A, Mimouni N, Heger A, Caldeira A, Hein J., Genome Res 18(2), 2008
PMID: 18073381
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution.
Janky R, van Helden J., BMC Bioinformatics 9(), 2008
PMID: 18215291
Janky R, van Helden J., BMC Bioinformatics 9(), 2008
PMID: 18215291
ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.
Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T., BMC Bioinformatics 9(), 2008
PMID: 18294369
Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T., BMC Bioinformatics 9(), 2008
PMID: 18294369
Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.
Margulies EH, Birney E., Nat Rev Genet 9(4), 2008
PMID: 18347593
Margulies EH, Birney E., Nat Rev Genet 9(4), 2008
PMID: 18347593
The cis-regulatory map of Shewanella genomes.
Liu J, Xu X, Stormo GD., Nucleic Acids Res 36(16), 2008
PMID: 18701645
Liu J, Xu X, Stormo GD., Nucleic Acids Res 36(16), 2008
PMID: 18701645
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation.
Varadarajan A, Bradley RK, Holmes IH., Genome Biol 9(10), 2008
PMID: 18840304
Varadarajan A, Bradley RK, Holmes IH., Genome Biol 9(10), 2008
PMID: 18840304
A model of evolution and structure for multiple sequence alignment.
Löytynoja A, Goldman N., Philos Trans R Soc Lond B Biol Sci 363(1512), 2008
PMID: 18852103
Löytynoja A, Goldman N., Philos Trans R Soc Lond B Biol Sci 363(1512), 2008
PMID: 18852103
How should gaps be treated in parsimony? A comparison of approaches using simulation.
Ogden TH, Rosenberg MS., Mol Phylogenet Evol 42(3), 2007
PMID: 17011794
Ogden TH, Rosenberg MS., Mol Phylogenet Evol 42(3), 2007
PMID: 17011794
Large-scale discovery of promoter motifs in Drosophila melanogaster.
Down TA, Bergman CM, Su J, Hubbard TJ., PLoS Comput Biol 3(1), 2007
PMID: 17238282
Down TA, Bergman CM, Su J, Hubbard TJ., PLoS Comput Biol 3(1), 2007
PMID: 17238282
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses.
Li L, Zhu Q, He X, Sinha S, Halfon MS., Genome Biol 8(6), 2007
PMID: 17550599
Li L, Zhu Q, He X, Sinha S, Halfon MS., Genome Biol 8(6), 2007
PMID: 17550599
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools.
Huang W, Nevins JR, Ohler U., Genome Biol 8(10), 2007
PMID: 17956628
Huang W, Nevins JR, Ohler U., Genome Biol 8(10), 2007
PMID: 17956628
Considerations in the identification of functional RNA structural elements in genomic alignments.
Babak T, Blencowe BJ, Hughes TR., BMC Bioinformatics 8(), 2007
PMID: 17263882
Babak T, Blencowe BJ, Hughes TR., BMC Bioinformatics 8(), 2007
PMID: 17263882
MySSP: non-stationary evolutionary sequence simulation, including indels.
Rosenberg MS., Evol Bioinform Online 1(), 2007
PMID: 19325855
Rosenberg MS., Evol Bioinform Online 1(), 2007
PMID: 19325855
Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes.
Alekseyenko AV, Kim N, Lee CJ., RNA 13(5), 2007
PMID: 17369312
Alekseyenko AV, Kim N, Lee CJ., RNA 13(5), 2007
PMID: 17369312
Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*.
Ogden TH, Rosenberg MS., Syst Biol 56(2), 2007
PMID: 17454974
Ogden TH, Rosenberg MS., Syst Biol 56(2), 2007
PMID: 17454974
Frequent gain and loss of functional transcription factor binding sites.
Doniger SW, Fay JC., PLoS Comput Biol 3(5), 2007
PMID: 17530920
Doniger SW, Fay JC., PLoS Comput Biol 3(5), 2007
PMID: 17530920
Molecular phylogenetics of the lizard genus Microlophus (squamata:tropiduridae): aligning and retrieving indel signal from nuclear introns.
Benavides E, Baum R, McClellan D, Sites JW., Syst Biol 56(5), 2007
PMID: 17907054
Benavides E, Baum R, McClellan D, Sites JW., Syst Biol 56(5), 2007
PMID: 17907054
How accurately is ncRNA aligned within whole-genome multiple alignments?
Wang AX, Ruzzo WL, Tompa M., BMC Bioinformatics 8(), 2007
PMID: 17963514
Wang AX, Ruzzo WL, Tompa M., BMC Bioinformatics 8(), 2007
PMID: 17963514
Accurate anchoring alignment of divergent sequences.
Huang W, Umbach DM, Li L., Bioinformatics 22(1), 2006
PMID: 16301203
Huang W, Umbach DM, Li L., Bioinformatics 22(1), 2006
PMID: 16301203
Evaluating phylogenetic footprinting for human-rodent comparisons.
Sauer T, Shelest E, Wingender E., Bioinformatics 22(4), 2006
PMID: 16332706
Sauer T, Shelest E, Wingender E., Bioinformatics 22(4), 2006
PMID: 16332706
Prediction of genomic functional elements.
Jones SJ., Annu Rev Genomics Hum Genet 7(), 2006
PMID: 16824019
Jones SJ., Annu Rev Genomics Hum Genet 7(), 2006
PMID: 16824019
SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools.
Shih AC, Lee DT, Lin L, Peng CL, Chen SH, Wu YW, Wong CY, Chou MY, Shiao TC, Hsieh MF., BMC Bioinformatics 7(), 2006
PMID: 16509994
Shih AC, Lee DT, Lin L, Peng CL, Chen SH, Wu YW, Wong CY, Chou MY, Shiao TC, Hsieh MF., BMC Bioinformatics 7(), 2006
PMID: 16509994
Multiple sequence alignment accuracy and phylogenetic inference.
Ogden TH, Rosenberg MS., Syst Biol 55(2), 2006
PMID: 16611602
Ogden TH, Rosenberg MS., Syst Biol 55(2), 2006
PMID: 16611602
Multiple sequence alignment with user-defined anchor points.
Morgenstern B, Prohaska SJ, Pöhler D, Stadler PF., Algorithms Mol Biol 1(1), 2006
PMID: 16722533
Morgenstern B, Prohaska SJ, Pöhler D, Stadler PF., Algorithms Mol Biol 1(1), 2006
PMID: 16722533
Conservation patterns in different functional sequence categories of divergent Drosophila species.
Papatsenko D, Kislyuk A, Levine M, Dubchak I., Genomics 88(4), 2006
PMID: 16697139
Papatsenko D, Kislyuk A, Levine M, Dubchak I., Genomics 88(4), 2006
PMID: 16697139
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison.
Halligan DL, Keightley PD., Genome Res 16(7), 2006
PMID: 16751341
Halligan DL, Keightley PD., Genome Res 16(7), 2006
PMID: 16751341
MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution.
Wang J, Keightley PD, Johnson T., BMC Bioinformatics 7(), 2006
PMID: 16762073
Wang J, Keightley PD, Johnson T., BMC Bioinformatics 7(), 2006
PMID: 16762073
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.
Pollard DA, Moses AM, Iyer VN, Eisen MB., BMC Bioinformatics 7(), 2006
PMID: 16904011
Pollard DA, Moses AM, Iyer VN, Eisen MB., BMC Bioinformatics 7(), 2006
PMID: 16904011
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes.
Uchiyama I, Higuchi T, Kobayashi I., BMC Bioinformatics 7(), 2006
PMID: 17062155
Uchiyama I, Higuchi T, Kobayashi I., BMC Bioinformatics 7(), 2006
PMID: 17062155
BlastAlign: a program that uses blast to align problematic nucleotide sequences.
Belshaw R, Katzourakis A., Bioinformatics 21(1), 2005
PMID: 15310559
Belshaw R, Katzourakis A., Bioinformatics 21(1), 2005
PMID: 15310559
Multiple sequence alignment with user-defined constraints at GOBICS.
Morgenstern B, Werner N, Prohaska SJ, Steinkamp R, Schneider I, Subramanian AR, Stadler PF, Weyer-Menkhoff J., Bioinformatics 21(7), 2005
PMID: 15546937
Morgenstern B, Werner N, Prohaska SJ, Steinkamp R, Schneider I, Subramanian AR, Stadler PF, Weyer-Menkhoff J., Bioinformatics 21(7), 2005
PMID: 15546937
Bases of motifs for generating repeated patterns with wild cards.
Pisanti N, Crochemore M, Grossi R, Sagot MF., IEEE/ACM Trans Comput Biol Bioinform 2(1), 2005
PMID: 17044163
Pisanti N, Crochemore M, Grossi R, Sagot MF., IEEE/ACM Trans Comput Biol Bioinform 2(1), 2005
PMID: 17044163
A model of the statistical power of comparative genome sequence analysis.
Eddy SR., PLoS Biol 3(1), 2005
PMID: 15660152
Eddy SR., PLoS Biol 3(1), 2005
PMID: 15660152
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.
Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B., BMC Bioinformatics 6(), 2005
PMID: 15784139
Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B., BMC Bioinformatics 6(), 2005
PMID: 15784139
Identification of functional transcription factor binding sites using closely related Saccharomyces species.
Doniger SW, Huh J, Fay JC., Genome Res 15(5), 2005
PMID: 15837806
Doniger SW, Huh J, Fay JC., Genome Res 15(5), 2005
PMID: 15837806
Evolutionary distance estimation and fidelity of pair wise sequence alignment.
Rosenberg MS., BMC Bioinformatics 6(), 2005
PMID: 15840174
Rosenberg MS., BMC Bioinformatics 6(), 2005
PMID: 15840174
A benchmark of multiple sequence alignment programs upon structural RNAs.
Gardner PP, Wilm A, Washietl S., Nucleic Acids Res 33(8), 2005
PMID: 15860779
Gardner PP, Wilm A, Washietl S., Nucleic Acids Res 33(8), 2005
PMID: 15860779
Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC.
Pöhler D, Werner N, Steinkamp R, Morgenstern B., Nucleic Acids Res 33(web server issue), 2005
PMID: 15980528
Pöhler D, Werner N, Steinkamp R, Morgenstern B., Nucleic Acids Res 33(web server issue), 2005
PMID: 15980528
Genomic multiple sequence alignments: refinement using a genetic algorithm.
Wang C, Lefkowitz EJ., BMC Bioinformatics 6(), 2005
PMID: 16086841
Wang C, Lefkowitz EJ., BMC Bioinformatics 6(), 2005
PMID: 16086841
Discovery of regulatory elements in vertebrates through comparative genomics.
Prakash A, Tompa M., Nat Biotechnol 23(10), 2005
PMID: 16211068
Prakash A, Tompa M., Nat Biotechnol 23(10), 2005
PMID: 16211068
Multiple sequence alignment accuracy and evolutionary distance estimation.
Rosenberg MS., BMC Bioinformatics 6(), 2005
PMID: 16305750
Rosenberg MS., BMC Bioinformatics 6(), 2005
PMID: 16305750
NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae.
Rambaldi D, Guffanti A, Morandi P, Cassata G., BMC Bioinformatics 6 Suppl 4(), 2005
PMID: 16351749
Rambaldi D, Guffanti A, Morandi P, Cassata G., BMC Bioinformatics 6 Suppl 4(), 2005
PMID: 16351749
ThurGood: evaluating assembly-to-assembly mapping.
Shatkay H, Miller J, Mobarry C, Flanigan M, Yooseph S, Sutton G., J Comput Biol 11(5), 2004
PMID: 15700403
Shatkay H, Miller J, Mobarry C, Flanigan M, Yooseph S, Sutton G., J Comput Biol 11(5), 2004
PMID: 15700403
Aligning multiple genomic sequences with the threaded blockset aligner.
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W., Genome Res 14(4), 2004
PMID: 15060014
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W., Genome Res 14(4), 2004
PMID: 15060014
Correction: Benchmarking tools for the alignment of functional noncoding DNA.
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB., BMC Bioinformatics 5(), 2004
PMID: 15186509
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB., BMC Bioinformatics 5(), 2004
PMID: 15186509
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ.
Morgenstern B., Nucleic Acids Res 32(web server issue), 2004
PMID: 15215344
Morgenstern B., Nucleic Acids Res 32(web server issue), 2004
PMID: 15215344
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences.
Brudno M, Steinkamp R, Morgenstern B., Nucleic Acids Res 32(web server issue), 2004
PMID: 15215346
Brudno M, Steinkamp R, Morgenstern B., Nucleic Acids Res 32(web server issue), 2004
PMID: 15215346
VISTA: computational tools for comparative genomics.
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I., Nucleic Acids Res 32(web server issue), 2004
PMID: 15215394
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I., Nucleic Acids Res 32(web server issue), 2004
PMID: 15215394
CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison.
Castrignanò T, Canali A, Grillo G, Liuni S, Mignone F, Pesole G., Nucleic Acids Res 32(web server issue), 2004
PMID: 15215464
Castrignanò T, Canali A, Grillo G, Liuni S, Mignone F, Pesole G., Nucleic Acids Res 32(web server issue), 2004
PMID: 15215464
Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA.
Nardone J, Lee DU, Ansel KM, Rao A., Nat Immunol 5(8), 2004
PMID: 15282556
Nardone J, Lee DU, Ansel KM, Rao A., Nat Immunol 5(8), 2004
PMID: 15282556
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE., Genome Biol 5(9), 2004
PMID: 15345045
Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE., Genome Biol 5(9), 2004
PMID: 15345045
DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors.
Schmollinger M, Nieselt K, Kaufmann M, Morgenstern B., BMC Bioinformatics 5(), 2004
PMID: 15357879
Schmollinger M, Nieselt K, Kaufmann M, Morgenstern B., BMC Bioinformatics 5(), 2004
PMID: 15357879
Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics.
Barnes DW, Mattingly CJ, Parton A, Dowell LM, Bayne CJ, Forrest JN., Cytotechnology 46(2-3), 2004
PMID: 19003267
Barnes DW, Mattingly CJ, Parton A, Dowell LM, Bayne CJ, Forrest JN., Cytotechnology 46(2-3), 2004
PMID: 19003267
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB., Genome Biol 5(12), 2004
PMID: 15575972
Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB., Genome Biol 5(12), 2004
PMID: 15575972
Bioinformatics: harvesting information for plant and crop science.
King GJ., Semin Cell Dev Biol 15(6), 2004
PMID: 15561592
King GJ., Semin Cell Dev Biol 15(6), 2004
PMID: 15561592
71 References
Daten bereitgestellt von Europe PubMed Central.
Comparison of genomic DNA sequences: solved and unsolved problems.
Miller W., Bioinformatics 17(5), 2001
PMID: 11331233
Miller W., Bioinformatics 17(5), 2001
PMID: 11331233
Cross-species sequence comparisons: a review of methods and available resources.
Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC., Genome Res. 13(1), 2003
PMID: 12529301
Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC., Genome Res. 13(1), 2003
PMID: 12529301
Comparative analysis of multiple protein-sequence alignment methods.
McClure MA, Vasi TK, Fitch WM., Mol. Biol. Evol. 11(4), 1994
PMID: 8078398
McClure MA, Vasi TK, Fitch WM., Mol. Biol. Evol. 11(4), 1994
PMID: 8078398
A comprehensive comparison of multiple sequence alignment programs.
Thompson JD, Plewniak F, Poch O., Nucleic Acids Res. 27(13), 1999
PMID: 10373585
Thompson JD, Plewniak F, Poch O., Nucleic Acids Res. 27(13), 1999
PMID: 10373585
Large-scale comparison of protein sequence alignment algorithms with structure alignments.
Sauder JM, Arthur JW, Dunbrack RL Jr., Proteins 40(1), 2000
PMID: 10813826
Sauder JM, Arthur JW, Dunbrack RL Jr., Proteins 40(1), 2000
PMID: 10813826
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.
Brenner SE, Chothia C, Hubbard TJ., Proc. Natl. Acad. Sci. U.S.A. 95(11), 1998
PMID: 9600919
Brenner SE, Chothia C, Hubbard TJ., Proc. Natl. Acad. Sci. U.S.A. 95(11), 1998
PMID: 9600919
AVID: A global alignment program.
Bray N, Dubchak I, Pachter L., Genome Res. 13(1), 2003
PMID: 12529311
Bray N, Dubchak I, Pachter L., Genome Res. 13(1), 2003
PMID: 12529311
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Program NC, Green ED, Sidow A, Batzoglou S., 2003
Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Program NC, Green ED, Sidow A, Batzoglou S., 2003
Rose: generating sequence families.
Stoye J, Evers D, Meyer F., Bioinformatics 14(2), 1998
PMID: 9545448
Stoye J, Evers D, Meyer F., Bioinformatics 14(2), 1998
PMID: 9545448
Application and accuracy of molecular phylogenies.
Hillis DM, Huelsenbeck JP, Cunningham CW., Science 264(5159), 1994
PMID: 8171318
Hillis DM, Huelsenbeck JP, Cunningham CW., Science 264(5159), 1994
PMID: 8171318
An evolutionary model for maximum likelihood alignment of DNA sequences.
Thorne JL, Kishino H, Felsenstein J., J. Mol. Evol. 33(2), 1991
PMID: 1920447
Thorne JL, Kishino H, Felsenstein J., J. Mol. Evol. 33(2), 1991
PMID: 1920447
Inching toward reality: an improved likelihood model of sequence evolution.
Thorne JL, Kishino H, Felsenstein J., J. Mol. Evol. 34(1), 1992
PMID: 1556741
Thorne JL, Kishino H, Felsenstein J., J. Mol. Evol. 34(1), 1992
PMID: 1556741
Dynamic programming alignment accuracy.
Holmes I, Durbin R., J. Comput. Biol. 5(3), 1998
PMID: 9773345
Holmes I, Durbin R., J. Comput. Biol. 5(3), 1998
PMID: 9773345
Multiple sequence alignment with the Divide-and-Conquer method.
Stoye J., Gene 211(2), 1998
PMID: 9669886
Stoye J., Gene 211(2), 1998
PMID: 9669886
Statistical alignment: computational properties, homology testing and goodness-of-fit.
Hein J, Wiuf C, Knudsen B, Moller MB, Wibling G., J. Mol. Biol. 302(1), 2000
PMID: 10964574
Hein J, Wiuf C, Knudsen B, Moller MB, Wibling G., J. Mol. Biol. 302(1), 2000
PMID: 10964574
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088
Quality assessment of multiple alignment programs.
Lassmann T, Sonnhammer EL., FEBS Lett. 529(1), 2002
PMID: 12354624
Lassmann T, Sonnhammer EL., FEBS Lett. 529(1), 2002
PMID: 12354624
Statistical alignment based on fragment insertion and deletion models.
Metzler D., Bioinformatics 19(4), 2003
PMID: 12611804
Metzler D., Bioinformatics 19(4), 2003
PMID: 12611804
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.
Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, Hodgson A, George RA, Hoskins RA, Laverty T, Muzny DM, Nelson CR, Pacleb JM, Park S, Pfeiffer BD, Richards S, Sodergren EJ, Svirskas R, Tabor PE, Wan K, Stapleton M, Sutton GG, Venter C, Weinstock G, Scherer SE, Myers EW, Gibbs RA, Rubin GM., Genome Biol. 3(12), 2002
PMID: 12537568
Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, Hodgson A, George RA, Hoskins RA, Laverty T, Muzny DM, Nelson CR, Pacleb JM, Park S, Pfeiffer BD, Richards S, Sodergren EJ, Svirskas R, Tabor PE, Wan K, Stapleton M, Sutton GG, Venter C, Weinstock G, Scherer SE, Myers EW, Gibbs RA, Rubin GM., Genome Biol. 3(12), 2002
PMID: 12537568
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE., Genome Biol. 3(12), 2002
PMID: 12537572
Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE., Genome Biol. 3(12), 2002
PMID: 12537572
Baylor College of Medicine Drosophila Genome Project
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
High intrinsic rate of DNA loss in Drosophila.
Petrov DA, Lozovskaya ER, Hartl DL., Nature 384(6607), 1996
PMID: 8934517
Petrov DA, Lozovskaya ER, Hartl DL., Nature 384(6607), 1996
PMID: 8934517
High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups.
Petrov DA, Hartl DL., Mol. Biol. Evol. 15(3), 1998
PMID: 9501496
Petrov DA, Hartl DL., Mol. Biol. Evol. 15(3), 1998
PMID: 9501496
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.
Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE., Genome Biol. 3(12), 2002
PMID: 12537573
Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE., Genome Biol. 3(12), 2002
PMID: 12537573
Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.
Bergman CM, Kreitman M., Genome Res. 11(8), 2001
PMID: 11483574
Bergman CM, Kreitman M., Genome Res. 11(8), 2001
PMID: 11483574
The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study.
Nekrutenko A, Makova KD, Li WH., Genome Res. 12(1), 2002
PMID: 11779845
Nekrutenko A, Makova KD, Li WH., Genome Res. 12(1), 2002
PMID: 11779845
Initial sequencing and comparative analysis of the mouse genome.
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES., Nature 420(6915), 2002
PMID: 12466850
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES., Nature 420(6915), 2002
PMID: 12466850
Genome evolution and developmental constraint in Caenorhabditis elegans.
Castillo-Davis CI, Hartl DL., Mol. Biol. Evol. 19(5), 2002
PMID: 11961106
Castillo-Davis CI, Hartl DL., Mol. Biol. Evol. 19(5), 2002
PMID: 11961106
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.
Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH., PLoS Biol. 1(2), 2003
PMID: 14624247
Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH., PLoS Biol. 1(2), 2003
PMID: 14624247
The molecular clock revisited: the rate of synonymous vs. replacement change in Drosophila.
Zeng LW, Comeron JM, Chen B, Kreitman M., Genetica 102-103(1-6), 1998
PMID: 9720289
Zeng LW, Comeron JM, Chen B, Kreitman M., Genetica 102-103(1-6), 1998
PMID: 9720289
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.
Bergman CM, Pfeiffer BD, Rincon-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, de Jong PJ, Botas J, Rubin GM, Celniker SE., Genome Biol. 3(12), 2002
PMID: 12537575
Bergman CM, Pfeiffer BD, Rincon-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, de Jong PJ, Botas J, Rubin GM, Celniker SE., Genome Biol. 3(12), 2002
PMID: 12537575
Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions.
Stoye J, Evers D, Meyer F., Proc Int Conf Intell Syst Mol Biol 5(), 1997
PMID: 9322053
Stoye J, Evers D, Meyer F., Proc Int Conf Intell Syst Mol Biol 5(), 1997
PMID: 9322053
How intron splicing affects the deletion and insertion profile in Drosophila melanogaster.
Ptak SE, Petrov DA., Genetics 162(3), 2002
PMID: 12454069
Ptak SE, Petrov DA., Genetics 162(3), 2002
PMID: 12454069
Comparative analyses of multi-species sequences from targeted genomic regions.
Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED., Nature 424(6950), 2003
PMID: 12917688
Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED., Nature 424(6950), 2003
PMID: 12917688
DIALIGN: finding local similarities by multiple sequence alignment.
Morgenstern B, Frech K, Dress A, Werner T., Bioinformatics 14(3), 1998
PMID: 9614273
Morgenstern B, Frech K, Dress A, Werner T., Bioinformatics 14(3), 1998
PMID: 9614273
Evidence for a high frequency of simultaneous double-nucleotide substitutions.
Averof M, Rokas A, Wolfe KH, Sharp PM., Science 287(5456), 2000
PMID: 10678838
Averof M, Rokas A, Wolfe KH, Sharp PM., Science 287(5456), 2000
PMID: 10678838
DNA sequence evolution with neighbor-dependent mutation.
Arndt PF, Burge CB, Hwa T., J. Comput. Biol. 10(3-4), 2003
PMID: 12935330
Arndt PF, Burge CB, Hwa T., J. Comput. Biol. 10(3-4), 2003
PMID: 12935330
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood
Siepel A, Haussler D., 2003
Siepel A, Haussler D., 2003
AlignmentBenchmarking
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Phylogenetic shadowing of primate sequences to find functional regions of the human genome.
Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM., Science 299(5611), 2003
PMID: 12610304
Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM., Science 299(5611), 2003
PMID: 12610304
Distinguishing regulatory DNA from neutral sites.
Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, Chiaromonte F., Genome Res. 13(1), 2003
PMID: 12529307
Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, Chiaromonte F., Genome Res. 13(1), 2003
PMID: 12529307
Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.
Cooper GM, Brudno M; NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A., Genome Res. 13(5), 2003
PMID: 12727901
Cooper GM, Brudno M; NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A., Genome Res. 13(5), 2003
PMID: 12727901
Evidence for stabilizing selection in a eukaryotic enhancer element.
Ludwig MZ, Bergman C, Patel NH, Kreitman M., Nature 403(6769), 2000
PMID: 10676967
Ludwig MZ, Bergman C, Patel NH, Kreitman M., Nature 403(6769), 2000
PMID: 10676967
Species-specific organization of CpG island promoters at mammalian homologous genes.
Cuadrado M, Sacristan M, Antequera F., EMBO Rep. 2(7), 2001
PMID: 11454739
Cuadrado M, Sacristan M, Antequera F., EMBO Rep. 2(7), 2001
PMID: 11454739
Turnover of binding sites for transcription factors involved in early Drosophila development.
Costas J, Casares F, Vieira J., Gene 310(), 2003
PMID: 12801649
Costas J, Casares F, Vieira J., Gene 310(), 2003
PMID: 12801649
Conservation of regulatory elements between two species of Drosophila.
Emberly E, Rajewsky N, Siggia ED., BMC Bioinformatics 4(), 2003
PMID: 14629780
Emberly E, Rajewsky N, Siggia ED., BMC Bioinformatics 4(), 2003
PMID: 14629780
An integrated computational pipeline and database to support whole-genome sequence annotation.
Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, Lewis SE., Genome Biol. 3(12), 2002
PMID: 12537570
Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, Lewis SE., Genome Biol. 3(12), 2002
PMID: 12537570
Comprehensive R Archive Network
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Weir BS., 1996
Over- and under-representation of short oligonucleotides in DNA sequences.
Burge C, Campbell AM, Karlin S., Proc. Natl. Acad. Sci. U.S.A. 89(4), 1992
PMID: 1741388
Burge C, Campbell AM, Karlin S., Proc. Natl. Acad. Sci. U.S.A. 89(4), 1992
PMID: 1741388
On some criteria for estimating the order of a Markov chain.
Katz RW., 1981
Katz RW., 1981
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.
Yang Z, Nielsen R., Mol. Biol. Evol. 17(1), 2000
PMID: 10666704
Yang Z, Nielsen R., Mol. Biol. Evol. 17(1), 2000
PMID: 10666704
PAML (version 3.13)
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa M, Kishino H, Yano T., J. Mol. Evol. 22(2), 1985
PMID: 3934395
Hasegawa M, Kishino H, Yano T., J. Mol. Evol. 22(2), 1985
PMID: 3934395
Codon usage bias and base composition of nuclear genes in Drosophila.
Moriyama EN, Hartl DL., Genetics 134(3), 1993
PMID: 8349115
Moriyama EN, Hartl DL., Genetics 134(3), 1993
PMID: 8349115
Intraspecific nuclear DNA variation in Drosophila.
Moriyama EN, Powell JR., Mol. Biol. Evol. 13(1), 1996
PMID: 8583899
Moriyama EN, Powell JR., Mol. Biol. Evol. 13(1), 1996
PMID: 8583899
The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces.
Comeron JM, Kreitman M., Genetics 156(3), 2000
PMID: 11063693
Comeron JM, Kreitman M., Genetics 156(3), 2000
PMID: 11063693
ROSE (version 1.3)
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Bayesian adaptive sequence alignment algorithms.
Zhu J, Liu JS, Lawrence CE., Bioinformatics 14(1), 1998
PMID: 9520499
Zhu J, Liu JS, Lawrence CE., Bioinformatics 14(1), 1998
PMID: 9520499
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences.
Tatusova TA, Madden TL., FEMS Microbiol. Lett. 174(2), 1999
PMID: 10339815
Tatusova TA, Madden TL., FEMS Microbiol. Lett. 174(2), 1999
PMID: 10339815
Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs.
Jareborg N, Birney E, Durbin R., Genome Res. 9(9), 1999
PMID: 10508839
Jareborg N, Birney E, Durbin R., Genome Res. 9(9), 1999
PMID: 10508839
Fast algorithms for large-scale genome alignment and comparison.
Delcher AL, Phillippy A, Carlton J, Salzberg SL., Nucleic Acids Res. 30(11), 2002
PMID: 12034836
Delcher AL, Phillippy A, Carlton J, Salzberg SL., Nucleic Acids Res. 30(11), 2002
PMID: 12034836
OWEN: aligning long collinear regions of genomes.
Ogurtsov AY, Roytberg MA, Shabalina SA, Kondrashov AS., Bioinformatics 18(12), 2002
PMID: 12490463
Ogurtsov AY, Roytberg MA, Shabalina SA, Kondrashov AS., Bioinformatics 18(12), 2002
PMID: 12490463
Improved tools for biological sequence comparison.
Pearson WR, Lipman DJ., Proc. Natl. Acad. Sci. U.S.A. 85(8), 1988
PMID: 3162770
Pearson WR, Lipman DJ., Proc. Natl. Acad. Sci. U.S.A. 85(8), 1988
PMID: 3162770
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
Needleman SB, Wunsch CD., J. Mol. Biol. 48(3), 1970
PMID: 5420325
Needleman SB, Wunsch CD., J. Mol. Biol. 48(3), 1970
PMID: 5420325
Human-mouse alignments with BLASTZ.
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W., Genome Res. 13(1), 2003
PMID: 12529312
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W., Genome Res. 13(1), 2003
PMID: 12529312
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern B., Bioinformatics 15(3), 1999
PMID: 10222408
Morgenstern B., Bioinformatics 15(3), 1999
PMID: 10222408
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson JD, Higgins DG, Gibson TJ., Nucleic Acids Res. 22(22), 1994
PMID: 7984417
Thompson JD, Higgins DG, Gibson TJ., Nucleic Acids Res. 22(22), 1994
PMID: 7984417
EMBOSS: the European Molecular Biology Open Software Suite.
Rice P, Longden I, Bleasby A., Trends Genet. 16(6), 2000
PMID: 10827456
Rice P, Longden I, Bleasby A., Trends Genet. 16(6), 2000
PMID: 10827456
Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment.
Kent WJ, Zahler AM., Genome Res. 10(8), 2000
PMID: 10958630
Kent WJ, Zahler AM., Genome Res. 10(8), 2000
PMID: 10958630
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