Data : The Benchmark Sequence : The Adh Region in D . melanogaster

Martin G. Reese, George Hartzell, Nomi L. Harris, Uwe Ohler, Josep F. Abril, and Suzanna E. Lewis Berkeley Drosophila Genome Project, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200 USA; Chair for Pattern Recognition, University of Erlangen–Nuremberg, D-91058 Erlangen, Germany;Institut Municipal d’Investigació Médica—Universitat Pompeu Fabra, Department of Medical Informatics (IMIM—UPF), 08003 Barcelona, Spain

[1]  Jonathan Pevsner,et al.  Basic Local Alignment Search Tool (BLAST) , 2005 .

[2]  Robert D. Finn,et al.  The Pfam protein families database , 2004, Nucleic Acids Res..

[3]  R. Durbin,et al.  Using GeneWise in the Drosophila annotation experiment. , 2000, Genome research.

[4]  R. Guigó,et al.  GeneID in Drosophila. , 2000, Genome research.

[5]  G. Stormo.  Gene-finding approaches for eukaryotes. , 2000, Genome research.

[6]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[7]  D. Haussler,et al.  Genie--gene finding in Drosophila melanogaster. , 2000, Genome research.

[8]  S Harbeck,et al.  Stochastic segment models of eukaryotic promoter regions. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[9]  D. Eisenberg,et al.  A combined algorithm for genome-wide prediction of protein function , 1999, Nature.

[10]  M. Borodovsky,et al.  Heuristic approach to deriving models for gene finding. , 1999, Nucleic acids research.

[11]  R George,et al.  An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. , 1999, Genetics.

[12]  Shmuel Pietrokovski,et al.  Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations , 1999, Bioinform..

[13]  Elmar Nöth,et al.  Interpolated markov chains for eukaryotic promoter recognition , 1999, Bioinform..

[14]  Stefan Kurtz,et al.  REPuter: fast computation of maximal repeats in complete genomes , 1999, Bioinform..

[15]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[16]  T. Hubbard,et al.  Critical assessment of methods of protein structure prediction (CASP): Round III , 1999 .

[17]  C Venclovas,et al.  Processing and analysis of CASP3 protein structure predictions , 1999, Proteins.

[18]  W A Koppensteiner,et al.  An attempt to analyse progress in fold recognition from CASP1 to CASP3 , 1999, Proteins.

[19]  Shmuel Pietrokovski,et al.  New features of the Blocks Database servers , 1999, Nucleic Acids Res..

[20]  Philipp Bucher,et al.  The Eukaryotic Promoter Database (EPD): recent developments , 1999, Nucleic Acids Res..

[21]  L D Stein,et al.  Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. , 1998, Genome research.

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

[23]  J. Jurka,et al.  Repeats in genomic DNA: mining and meaning. , 1998, Current opinion in structural biology.

[24]  S. Karlin,et al.  Finding the genes in genomic DNA. , 1998, Current opinion in structural biology.

[25]  Sean R. Eddy,et al.  Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..

[26]  Philipp Bucher,et al.  The Eukaryotic Promoter Database EPD , 1998, Nucleic Acids Res..

[27]  Pankaj Agarwal,et al.  Comparative accuracy of methods for protein sequence similarity search , 1998, Bioinform..

[28]  J. Fickett,et al.  Eukaryotic promoter recognition. , 1997, Genome research.

[29]  Richard Mott,et al.  EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA , 1997, Comput. Appl. Biosci..

[30]  R. Durbin,et al.  Pfam: A comprehensive database of protein domain families based on seed alignments , 1997, Proteins.

[31]  Ewan Birney,et al.  Dynamite: A Flexible Code Generating Language for Dynamic Programming Methods Used in Sequence Comparison , 1997, ISMB.

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

[33]  Roland L. Dunbrack,et al.  Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996. , 1997, Folding & design.

[34]  David Haussler,et al.  Improved splice site detection in Genie , 1997, RECOMB '97.

[35]  S. Bryant,et al.  Critical assessment of methods of protein structure prediction (CASP): Round II , 1997, Proteins.

[36]  M Levitt,et al.  Competitive assessment of protein fold recognition and alignment accuracy , 1997, Proteins.

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

[38]  A. Krogh.  Two methods for improving performance of an HMM application for gene finding , 1997 .

[39]  R. Guigó,et al.  Evaluation of gene structure prediction programs. , 1996, Genomics.

[40]  T Gaasterland,et al.  MAGPIE: automated genome interpretation. , 1996, Trends in genetics : TIG.

[41]  W. Pearson.  Comparison of methods for searching protein sequence databases , 1995, Protein science : a publication of the Protein Society.

[42]  I. Arkhipova,et al.  Promoter elements in Drosophila melanogaster revealed by sequence analysis. , 1995, Genetics.

[43]  R. Durbin,et al.  ACeDB and macace. , 1995, Methods in cell biology.

[44]  Victor V. Solovyev,et al.  Identification of Human Gene Structure Using Linear Discriminant Functions and Dynamic Programming , 1995, ISMB.

[45]  S. Henikoff,et al.  Protein family classification based on searching a database of blocks. , 1994, Genomics.

[46]  J. Fickett,et al.  Assessment of protein coding measures. , 1992, Nucleic acids research.

[47]  Temple F. Smith,et al.  Prediction of gene structure. , 1992, Journal of molecular biology.

[48]  E. Uberbacher,et al.  Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[49]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.