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EST entries from dbEST for model organisms

 

 

List of references on EST data and Analysis

  1. Altschul, S. F., W. Gish, et al. (1990). "Basic local alignment search tool." J Mol Biol 215(3): 403-10.
  2. Adams, M. D., J. M. Kelley, et al. (1991). "Complementary DNA sequencing: expressed sequence tags and human genome project." Science 252(5013): 1651-6.
  3. Wilcox, A. S., A. S. Khan, et al. (1991). "Use of 3' untranslated sequences of human cDNAs for rapid chromosome assignment and conversion to STSs: implications for an expression map of the genome." Nucleic Acids Res 19(8): 1837-43.
  4. Boguski, M. S., T. M. Lowe, et al. (1993). "dbEST--database for "expressed sequence tags"." Nat Genet 4(4): 332-3.
  5. Boguski, M. S. and G. D. Schuler (1995). "ESTablishing a human transcript map." Nat Genet 10(4): 369-71.
  6. Aaronson, J. S., B. Eckman, et al. (1996). "Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data." Genome Res 6(9): 829-45.
  7. Bonaldo, M. F., G. Lennon, et al. (1996). "Normalization and subtraction: two approaches to facilitate gene discovery." Genome Res 6(9): 791-806.
  8. Hillier, L. D., G. Lennon, et al. (1996). "Generation and analysis of 280,000 human expressed sequence tags." Genome Res 6(9): 807-28.
  9. Altschul, S. F., T. L. Madden, et al. (1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res 25(17): 3389-402.
  10. Burke, J., H. Wang, et al. (1998). "Alternative gene form discovery and candidate gene selection from gene indexing projects." Genome Res 8(3): 276-90.
  11. Eckman, B. A., J. S. Aaronson, et al. (1998). "The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining." Bioinformatics 14(1): 2-13.
  12. Ewing, B. and P. Green (1998). "Base-calling of automated sequencer traces using phred. II. Error probabilities." Genome Res 8(3): 186-94.
  13. Ewing, B., L. Hillier, et al. (1998). "Base-calling of automated sequencer traces using phred. I. Accuracy assessment." Genome Res 8(3): 175-85.
  14. Florea, L., G. Hartzell, et al. (1998). "A computer program for aligning a cDNA sequence with a genomic DNA sequence." Genome Res 8(9): 967-74.
  15. Gautheret, D., O. Poirot, et al. (1998). "Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering." Genome Res 8(5): 524-30.
  16. Jiang, J. and H. J. Jacob (1998). "EbEST: an automated tool using expressed sequence tags to delineate gene structure." Genome Res 8(3): 268-75.
  17. Buetow, K. H., M. N. Edmonson, et al. (1999). "Reliable identification of large numbers of candidate SNPs from public EST data." Nat Genet 21(3): 323-5.
  18. Burke, J., D. Davison, et al. (1999). "d2_cluster: a validated method for clustering EST and full-length cDNAsequences." Genome Res 9(11): 1135-42.
  19. Ewing, R. M., A. Ben Kahla, et al. (1999). "Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression." Genome Res 9(10): 950-9.
  20. Hawkins, V., D. Doll, et al. (1999). "PEDB: the Prostate Expression Database." Nucleic Acids Res 27(1): 204-8.
  21. Heyer, L. J., S. Kruglyak, et al. (1999). "Exploring expression data: identification and analysis of coexpressed genes." Genome Res 9(11): 1106-15.
  22. Huang, X. and A. Madan (1999). "CAP3: A DNA sequence assembly program." Genome Res 9(9): 868-77.
  23. Iseli, C., C. V. Jongeneel, et al. (1999). "ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences." Proc Int Conf Intell Syst Mol Biol: 138-48.
  24. Miller, R. T., A. G. Christoffels, et al. (1999). "A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base." Genome Res 9(11): 1143-55.
  25. Mironov, A. A., J. W. Fickett, et al. (1999). "Frequent alternative splicing of human genes." Genome Res 9(12): 1288-93.
  26. Picoult-Newberg, L., T. E. Ideker, et al. (1999). "Mining SNPs from EST databases." Genome Res 9(2): 167-74.
  27. Schmitt, A. O., T. Specht, et al. (1999). "Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues." Nucleic Acids Res 27(21): 4251-60.
  28. Bedell, J. A., I. Korf, et al. (2000). "MaskerAid: a performance enhancement to RepeatMasker." Bioinformatics 16(11): 1040-1.
  29. Brett, D., J. Hanke, et al. (2000). "EST comparison indicates 38% of human mRNAs contain possible alternative splice forms." FEBS Lett 474(1): 83-6.
  30. Croft, L., S. Schandorff, et al. (2000). "ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome." Nat Genet 24(4): 340-1.
  31. Cuff, J. A., E. Birney, et al. (2000). "ProtEST: protein multiple sequence alignments from expressed sequence tags." Bioinformatics 16(2): 111-6.
  32. Liang, F., I. Holt, et al. (2000). "An optimized protocol for analysis of EST sequences." Nucleic Acids Res 28(18): 3657-65.
  33. Parsons, J. D. and P. Rodriguez-Tome (2000). "JESAM: CORBA software components to create and publish EST alignments and clusters." Bioinformatics 16(4): 313-25.
  34. Quackenbush, J., F. Liang, et al. (2000). "The TIGR gene indices: reconstruction and representation of expressed gene sequences." Nucleic Acids Res 28(1): 141-5.
  35. Usuka, J., W. Zhu, et al. (2000). "Optimal spliced alignment of homologous cDNA to a genomic DNA template." Bioinformatics 16(3): 203-11.
  36. Chou, H. H. and M. H. Holmes (2001). "DNA sequence quality trimming and vector removal." Bioinformatics 17(12): 1093-104.
  37. Fukunishi, Y. and Y. Hayashizaki (2001). "Amino acid translation program for full-length cDNA sequences with frameshift errors." Physiol Genomics 5(2): 81-7.
  38. Kan, Z., E. C. Rouchka, et al. (2001). "Gene structure prediction and alternative splicing analysis using genomically aligned ESTs." Genome Res 11(5): 889-900.
  39. Lisacek, F. C., M. D. Traini, et al. (2001). "Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting." Proteomics 1(2): 186-93.
  40. Modrek, B., A. Resch, et al. (2001). "Genome-wide detection of alternative splicing in expressed sequences of human genes." Nucleic Acids Res 29(13): 2850-9.
  41. Quackenbush, J., J. Cho, et al. (2001). "The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species." Nucleic Acids Res 29(1): 159-64.
  42. Zdobnov, E. M. and R. Apweiler (2001). "InterProScan--an integration platform for the signature-recognition methods in InterPro." Bioinformatics 17(9): 847-8.
  43. Ayoubi, P., X. Jin, et al. (2002). "PipeOnline 2.0: automated EST processing and functional data sorting." Nucleic Acids Res 30(21): 4761-9.
  44. Bennetzen, J. L. (2002). "Mechanisms and rates of genome expansion and contraction in flowering plants." Genetica 115(1): 29-36.
  45. Carpenter, J. E., A. Christoffels, et al. (2002). "Assessment of the parallelization approach of d2_cluster for high-performance sequence clustering." J Comput Chem 23(7): 755-7.
  46. Parkinson, J., D. B. Guiliano, et al. (2002). "Making sense of EST sequences by CLOBBing them." BMC Bioinformatics 3: 31.
  47. Waterston, R. H., K. Lindblad-Toh, et al. (2002). "Initial sequencing and comparative analysis of the mouse genome." Nature 420(6915): 520-62.
  48. Hotz-Wagenblatt, A., T. Hankeln, et al. (2003). "ESTAnnotator: A tool for high throughput EST annotation." Nucleic Acids Res 31(13): 3716-9.
  49. Kim, S. I., J. Y. Kim, et al. (2003). "Proteome analysis of hairy root from Panax ginseng C.A. Meyer using peptide fingerprinting, internal sequencing and expressed sequence tag data." Proteomics 3(12): 2379-92.
  50. Lee, B. T., T. W. Tan, et al. (2003). "MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences." Nucleic Acids Res 31(13): 3533-6.
  51. Mao, C., J. C. Cushman, et al. (2003). "ESTAP--an automated system for the analysis of EST data." Bioinformatics 19(13): 1720-2.
  52. Paquola, A. C., M. Y. Nishyiama, Jr., et al. (2003). "ESTWeb: bioinformatics services for EST sequencing projects." Bioinformatics 19(12): 1587-8.
  53. Parkinson, J., M. Mitreva, et al. (2003). "400000 nematode ESTs on the Net." Trends Parasitol 19(7): 283-6.
  54. Pertea, G., X. Huang, et al. (2003). "TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets." Bioinformatics 19(5): 651-2.
  55. Rudd, S. (2003). "Expressed sequence tags: alternative or complement to whole genome sequences?" Trends Plant Sci 8(7): 321-9.
  56. Wan, H., L. Li, et al. (2003). "Discovering simple regions in biological sequences associated with scoring schemes." J Comput Biol 10(2): 171-85.
  57. Brendel, V., L. Xing, et al. (2004). "Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus." Bioinformatics 20(7): 1157-69.
  58. Chen, Y. A., D. J. McKillen, et al. (2004). "Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information." BMC Bioinformatics 5(1): 191.
  59. Chevreux, B., T. Pfisterer, et al. (2004). "Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs." Genome Res 14(6): 1147-59.
  60. Curwen, V., E. Eyras, et al. (2004). "The Ensembl automatic gene annotation system." Genome Res 14(5): 942-50.
  61. Eyras, E., M. Caccamo, et al. (2004). "ESTGenes: alternative splicing from ESTs in Ensembl." Genome Res 14(5): 976-87.
  62. Kan, Z., J. Castle, et al. (2004). "Detection of novel splice forms in human and mouse using cross-species approach." Pac Symp Biocomput: 42-53.
  63. Kumar, C. G., R. LeDuc, et al. (2004). "ESTIMA, a tool for EST management in a multi-project environment." BMC Bioinformatics 5: 176.
  64. Li, S. and H. H. Chou (2004). "LUCY2: an interactive DNA sequence quality trimming and vector removal tool." Bioinformatics 20(16): 2865-6.
  65. Nilsson, R. H., B. Rajashekar, et al. (2004). "galaxieEST: addressing EST identity through automated phylogenetic analysis." BMC Bioinformatics 5: 87.
  66. Parkinson, J., A. Anthony, et al. (2004). "PartiGene--constructing partial genomes." Bioinformatics 20(9): 1398-404.
  67. Parkinson, J., C. Whitton, et al. (2004). "NEMBASE: a resource for parasitic nematode ESTs." Nucleic Acids Res 32(Database issue): D427-30.
  68. Wasmuth, J. D. and M. L. Blaxter (2004). "prot4EST: translating expressed sequence tags from neglected genomes." BMC Bioinformatics 5(1): 187.
  69. Wylie, T., J. C. Martin, et al. (2004). "Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes." Nucleic Acids Res 32(Database issue): D423-6.
  70. Dong, Q., L. Kroiss, et al. (2005). "Comparative EST analyses in plant systems." Methods Enzymol 395: 400-18.
  71. Huang, Y., J. Pumphrey, et al. (2005). "ESTminer: a Web interface for mining EST contig and cluster databases." Bioinformatics 21(5): 669-70.
  72. Kim, P., N. Kim, et al. (2005). "ECgene: genome annotation for alternative splicing." Nucleic Acids Res 33(Database issue): D75-9.
  73. Kunne, C., M. Lange, et al. (2005). "CR-EST: a resource for crop ESTs." Nucleic Acids Res 33(Database issue): D619-21.
  74. Lee, Y., J. Tsai, et al. (2005). "The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes." Nucleic Acids Res 33(Database issue): D71-4.
  75. Maheswari, U., A. Montsant, et al. (2005). "The Diatom EST Database." Nucleic Acids Res 33(Database issue): D344-7.
  76. Malde, K., E. Coward, et al. (2005). "A graph based algorithm for generating EST consensus sequences." Bioinformatics 21(8): 1371-5.
  77. Min, X. J., G. Butler, et al. (2005). "OrfPredictor: predicting protein-coding regions in EST-derived sequences." Nucleic Acids Res 33(Web Server issue): W677-80.
  78. Nelson, R. T., D. Grant, et al. (2005). "ESTminer: a suite of programs for gene and allele identification." Bioinformatics 21(5): 691-3.
  79. Ptitsyn, A. and W. Hide (2005). "CLU: a new algorithm for EST clustering." BMC Bioinformatics 6 Suppl 2: S3.
  80. Quevillon, E., V. Silventoinen, et al. (2005). "InterProScan: protein domains identifier." Nucleic Acids Res 33(Web Server issue): W116-20.
  81. Rudd, S. (2005). "openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections." Nucleic Acids Res 33(Database issue): D622-7.