TY - JOUR AU - Stark, A. AU - Lin, M. F. AU - Kheradpour, P. AU - Pedersen, J. S. AU - Parts, L. AU - Carlson, J. W. AU - Crosby, M. A. AU - Rasmussen, M. D. AU - Roy, S. AU - Deoras, A. N. PY - 2007 DA - 2007// TI - Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures JO - Nature VL - 450 UR - https://doi.org/10.1038/nature06340 DO - 10.1038/nature06340 ID - Stark2007 ER - TY - JOUR AU - Yuh, C. H. AU - Brown, C. T. AU - Livi, C. B. AU - Rowen, L. AU - Clarke, P. J. AU - Davidson, E. H. PY - 2002 DA - 2002// TI - Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin JO - Dev Biol VL - 246 UR - https://doi.org/10.1006/dbio.2002.0618 DO - 10.1006/dbio.2002.0618 ID - Yuh2002 ER - TY - JOUR AU - Friedman, R. C. AU - Farh, K. K. AU - Burge, C. B. AU - Bartel, D. P. PY - 2009 DA - 2009// TI - Most mammalian mRNAs are conserved targets of microRNAs JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.082701.108 DO - 10.1101/gr.082701.108 ID - Friedman2009 ER - TY - JOUR AU - Janecka, J. E. AU - Miller, W. AU - Pringle, T. H. AU - Wiens, F. AU - Zitzmann, A. AU - Helgen, K. M. AU - Springer, M. S. AU - Murphy, W. J. PY - 2007 DA - 2007// TI - Molecular and genomic data identify the closest living relative of primates JO - Science VL - 318 UR - https://doi.org/10.1126/science.1147555 DO - 10.1126/science.1147555 ID - Janecka2007 ER - TY - JOUR AU - Treangen, T. J. AU - Messeguer, X. PY - 2006 DA - 2006// TI - M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-433 DO - 10.1186/1471-2105-7-433 ID - Treangen2006 ER - TY - JOUR AU - Schwartz, S. AU - Kent, W. J. AU - Smit, A. AU - Zhang, Z. AU - Baertsch, R. AU - Hardison, R. C. AU - Haussler, D. AU - Miller, W. PY - 2003 DA - 2003// TI - Human-mouse alignments with BLASTZ JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.809403 DO - 10.1101/gr.809403 ID - Schwartz2003 ER - TY - JOUR AU - Karolchik, D. AU - Kuhn, R. M. AU - Baertsch, R. AU - Barber, G. P. AU - Clawson, H. AU - Diekhans, M. AU - Giardine, B. AU - Harte, R. A. AU - Hinrichs, A. S. AU - Hsu, F. PY - 2008 DA - 2008// TI - The UCSC Genome Browser Database: 2008 update JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm966 DO - 10.1093/nar/gkm966 ID - Karolchik2008 ER - TY - CHAP AU - Chiaromonte, F. AU - Yap, V. B. AU - Miller, W. PY - 2002 DA - 2002// TI - Scoring pairwise genomic sequence alignments BT - Pac Symp Biocomput ID - Chiaromonte2002 ER - TY - JOUR AU - Karlin, S. AU - Altschul, S. F. PY - 1990 DA - 1990// TI - Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes JO - Proc Natl Acad Sci USA VL - 87 UR - https://doi.org/10.1073/pnas.87.6.2264 DO - 10.1073/pnas.87.6.2264 ID - Karlin1990 ER - TY - JOUR AU - Altschul, S. F. PY - 1991 DA - 1991// TI - Amino acid substitution matrices from an information theoretic perspective JO - J Mol Biol VL - 219 UR - https://doi.org/10.1016/0022-2836(91)90193-A DO - 10.1016/0022-2836(91)90193-A ID - Altschul1991 ER - TY - JOUR AU - States, D. AU - Gish, W. AU - Altschul, S. PY - 1991 DA - 1991// TI - Improved sensitivity of nucleic acid database searches using application-specific scoring matrices JO - Methods VL - 3 UR - https://doi.org/10.1016/S1046-2023(05)80165-3 DO - 10.1016/S1046-2023(05)80165-3 ID - States1991 ER - TY - BOOK AU - Durbin, R. AU - Eddy, S. AU - Krogh, A. AU - Mitchison, G. PY - 1999 DA - 1999// TI - Biological Sequence Analysis PB - Cambridge University Press CY - Cambridge ID - Durbin1999 ER - TY - JOUR AU - Reese, J. T. AU - Pearson, W. R. PY - 2002 DA - 2002// TI - Empirical determination of effective gap penalties for sequence comparison JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.11.1500 DO - 10.1093/bioinformatics/18.11.1500 ID - Reese2002 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Zhang, Z. AU - Berman, P. AU - Wiehe, T. AU - Miller, W. PY - 1999 DA - 1999// TI - Post-processing long pairwise alignments JO - Bioinformatics VL - 15 UR - https://doi.org/10.1093/bioinformatics/15.12.1012 DO - 10.1093/bioinformatics/15.12.1012 ID - Zhang1999 ER - TY - JOUR AU - Lunter, G. AU - Rocco, A. AU - Mimouni, N. AU - Heger, A. AU - Caldeira, A. AU - Hein, J. PY - 2008 DA - 2008// TI - Uncertainty in homology inferences: assessing and improving genomic sequence alignment JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.6725608 DO - 10.1101/gr.6725608 ID - Lunter2008 ER - TY - JOUR AU - Wong, K. M. AU - Suchard, M. A. AU - Huelsenbeck, J. P. PY - 2008 DA - 2008// TI - Alignment uncertainty and genomic analysis JO - Science VL - 319 UR - https://doi.org/10.1126/science.1151532 DO - 10.1126/science.1151532 ID - Wong2008 ER - TY - JOUR AU - Miyazawa, S. PY - 1995 DA - 1995// TI - A reliable sequence alignment method based on probabilities of residue correspondences JO - Protein Eng VL - 8 UR - https://doi.org/10.1093/protein/8.10.999 DO - 10.1093/protein/8.10.999 ID - Miyazawa1995 ER - TY - JOUR AU - Brudno, M. AU - Poliakov, A. AU - Salamov, A. AU - Cooper, G. M. AU - Sidow, A. AU - Rubin, E. M. AU - Solovyev, V. AU - Batzoglou, S. AU - Dubchak, I. PY - 2004 DA - 2004// TI - Automated whole-genome multiple alignment of rat, mouse, and human JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2067704 DO - 10.1101/gr.2067704 ID - Brudno2004 ER - TY - JOUR AU - Huang, W. AU - Umbach, D. M. AU - Li, L. PY - 2006 DA - 2006// TI - Accurate anchoring alignment of divergent sequences JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti772 DO - 10.1093/bioinformatics/bti772 ID - Huang2006 ER - TY - JOUR AU - Pollard, D. A. AU - Bergman, C. M. AU - Stoye, J. AU - Celniker, S. E. AU - Eisen, M. B. PY - 2004 DA - 2004// TI - Correction: Benchmarking tools for the alignment of functional noncoding DNA JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-73 DO - 10.1186/1471-2105-5-73 ID - Pollard2004 ER - TY - JOUR AU - Margulies, E. H. AU - Cooper, G. M. AU - Asimenos, G. AU - Thomas, D. J. AU - Dewey, C. N. AU - Siepel, A. AU - Birney, E. AU - Keefe, D. AU - Schwartz, A. S. AU - Hou, M. PY - 2007 DA - 2007// TI - Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6034307 DO - 10.1101/gr.6034307 ID - Margulies2007 ER - TY - JOUR AU - Kriegs, J. O. AU - Churakov, G. AU - Jurka, J. AU - Brosius, J. AU - Schmitz, J. PY - 2007 DA - 2007// TI - Evolutionary history of 7SL RNA-derived SINEs in Supraprimates JO - Trends Genet VL - 23 UR - https://doi.org/10.1016/j.tig.2007.02.002 DO - 10.1016/j.tig.2007.02.002 ID - Kriegs2007 ER - TY - JOUR AU - Benson, G. PY - 1999 DA - 1999// TI - Tandem repeats finder: a program to analyze DNA sequences JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.2.573 DO - 10.1093/nar/27.2.573 ID - Benson1999 ER - TY - JOUR AU - Morgulis, A. AU - Gertz, E. M. AU - Schäffer, A. A. AU - Agarwala, R. PY - 2006 DA - 2006// TI - A fast and symmetric DUST implementation to mask low-complexity DNA sequences JO - J Comput Biol VL - 13 UR - https://doi.org/10.1089/cmb.2006.13.1028 DO - 10.1089/cmb.2006.13.1028 ID - Morgulis2006 ER - TY - JOUR AU - Wootton, J. C. AU - Federhen, S. PY - 1996 DA - 1996// TI - Analysis of compositionally biased regions in sequence databases JO - Methods Enzymol VL - 266 UR - https://doi.org/10.1016/S0076-6879(96)66035-2 DO - 10.1016/S0076-6879(96)66035-2 ID - Wootton1996 ER - TY - JOUR AU - Morgulis, A. AU - Gertz, E. M. AU - Schäffer, A. A. AU - Agarwala, R. PY - 2006 DA - 2006// TI - WindowMasker: window-based masker for sequenced genomes JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti774 DO - 10.1093/bioinformatics/bti774 ID - Morgulis2006 ER - TY - JOUR AU - Gardner, P. P. AU - Daub, J. AU - Tate, J. G. AU - Nawrocki, E. P. AU - Kolbe, D. L. AU - Lindgreen, S. AU - Wilkinson, A. C. AU - Finn, R. D. AU - Griffiths-Jones, S. AU - Eddy, S. R. AU - Bateman, A. PY - 2009 DA - 2009// TI - Rfam: updates to the RNA families database JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn766 DO - 10.1093/nar/gkn766 ID - Gardner2009 ER - TY - JOUR AU - Ruan, J. AU - Li, H. AU - Chen, Z. AU - Coghlan, A. AU - Coin, L. J. AU - Guo, Y. AU - Hériché, J. K. AU - Hu, Y. AU - Kristiansen, K. AU - Li, R. PY - 2008 DA - 2008// TI - TreeFam: 2008 Update JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm1005 DO - 10.1093/nar/gkm1005 ID - Ruan2008 ER - TY - JOUR AU - Frith, M. C. AU - Park, Y. AU - Sheetlin, S. L. AU - Spouge, J. L. PY - 2008 DA - 2008// TI - The whole alignment and nothing but the alignment: the problem of spurious alignment flanks JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn579 DO - 10.1093/nar/gkn579 ID - Frith2008 ER - TY - JOUR AU - Carvalho, L. E. AU - Lawrence, C. E. PY - 2008 DA - 2008// TI - Centroid estimation in discrete high-dimensional spaces with applications in biology JO - Proc Natl Acad Sci USA VL - 105 UR - https://doi.org/10.1073/pnas.0712329105 DO - 10.1073/pnas.0712329105 ID - Carvalho2008 ER - TY - CHAP AU - Schwartz, A. AU - Myers, E. AU - Pachter, L. PY - 2005 DA - 2005// BT - Alignment Metric Accuracy ID - Schwartz2005 ER - TY - JOUR AU - Hamada, M. AU - Kiryu, H. AU - Sato, K. AU - Mituyama, T. AU - Asai, K. PY - 2009 DA - 2009// TI - Prediction of RNA secondary structure using generalized centroid estimators JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btn601 DO - 10.1093/bioinformatics/btn601 ID - Hamada2009 ER - TY - JOUR AU - Holmes, I. AU - Durbin, R. PY - 1998 DA - 1998// TI - Dynamic programming alignment accuracy JO - J Comput Biol VL - 5 UR - https://doi.org/10.1089/cmb.1998.5.493 DO - 10.1089/cmb.1998.5.493 ID - Holmes1998 ER - TY - JOUR AU - Kent, W. J. AU - Zahler, A. M. PY - 2000 DA - 2000// TI - Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment JO - Genome Res VL - 10 UR - https://doi.org/10.1101/gr.10.8.1115 DO - 10.1101/gr.10.8.1115 ID - Kent2000 ER - TY - JOUR AU - Lunter, G. PY - 2007 DA - 2007// TI - Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm185 DO - 10.1093/bioinformatics/btm185 ID - Lunter2007 ER - TY - JOUR AU - Newberg, L. A. AU - Lawrence, C. E. PY - 2009 DA - 2009// TI - Exact calculation of distributions on integers, with application to sequence alignment JO - J Comput Biol VL - 16 UR - https://doi.org/10.1089/cmb.2008.0137 DO - 10.1089/cmb.2008.0137 ID - Newberg2009 ER - TY - JOUR AU - Sheetlin, S. AU - Park, Y. AU - Spouge, J. L. PY - 2005 DA - 2005// TI - The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki800 DO - 10.1093/nar/gki800 ID - Sheetlin2005 ER - TY - JOUR AU - Paten, B. AU - Herrero, J. AU - Beal, K. AU - Fitzgerald, S. AU - Birney, E. PY - 2008 DA - 2008// TI - Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.076554.108 DO - 10.1101/gr.076554.108 ID - Paten2008 ER - TY - JOUR AU - Wang, J. AU - Keightley, P. D. AU - Johnson, T. PY - 2006 DA - 2006// TI - MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-292 DO - 10.1186/1471-2105-7-292 ID - Wang2006 ER - TY - JOUR AU - Bradley, R. K. AU - Roberts, A. AU - Smoot, M. AU - Juvekar, S. AU - Do, J. AU - Dewey, C. AU - Holmes, I. AU - Pachter, L. PY - 2009 DA - 2009// TI - Fast statistical alignment JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000392 DO - 10.1371/journal.pcbi.1000392 ID - Bradley2009 ER - TY - JOUR AU - Kumar, S. AU - Filipski, A. PY - 2007 DA - 2007// TI - Multiple sequence alignment: in pursuit of homologous DNA positions JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5232407 DO - 10.1101/gr.5232407 ID - Kumar2007 ER - TY - JOUR AU - Waterman, M. S. AU - Eggert, M. AU - Lander, E. PY - 1992 DA - 1992// TI - Parametric sequence comparisons JO - Proc Natl Acad Sci USA VL - 89 UR - https://doi.org/10.1073/pnas.89.13.6090 DO - 10.1073/pnas.89.13.6090 ID - Waterman1992 ER - TY - JOUR AU - Dewey, C. N. AU - Huggins, P. M. AU - Woods, K. AU - Sturmfels, B. AU - Pachter, L. PY - 2006 DA - 2006// TI - Parametric alignment of Drosophila genomes JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020073 DO - 10.1371/journal.pcbi.0020073 ID - Dewey2006 ER - TY - JOUR AU - Gusfield, D. AU - Stelling, P. PY - 1996 DA - 1996// TI - Parametric and inverse-parametric sequence alignment with XPARAL JO - Methods Enzymol VL - 266 UR - https://doi.org/10.1016/S0076-6879(96)66030-3 DO - 10.1016/S0076-6879(96)66030-3 ID - Gusfield1996 ER - TY - JOUR AU - Kim, E. AU - Kececioglu, J. PY - 2008 DA - 2008// TI - Learning scoring schemes for sequence alignment from partial examples JO - IEEE/ACM Trans Comput Biol Bioinform VL - 5 UR - https://doi.org/10.1109/TCBB.2008.57 DO - 10.1109/TCBB.2008.57 ID - Kim2008 ER - TY - JOUR AU - Pruitt, K. D. AU - Tatusova, T. AU - Maglott, D. R. PY - 2007 DA - 2007// TI - NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl842 DO - 10.1093/nar/gkl842 ID - Pruitt2007 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - BLAT--the BLAST-like alignment tool JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229202. Article published online before March 2002 DO - 10.1101/gr.229202. Article published online before March 2002 ID - Kent2002 ER - TY - JOUR AU - Yu, Y. K. AU - Wootton, J. C. AU - Altschul, S. F. PY - 2003 DA - 2003// TI - The compositional adjustment of amino acid substitution matrices JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.2533904100 DO - 10.1073/pnas.2533904100 ID - Yu2003 ER -