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EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA
Abstract
spliced DNA to unspliced genomic DNA. It is written in ANSI C and has been tested under Digital OSF3.2. The spurce code and documentation are available from ftp:// www.sanger.ac.uky ftp/pub / badger/est_genome.2.tar.Z. The prediction of genes in uncharacterized genomic DNA sequence is currently one of the main problems facing sequence annotators. Methods based on de novo prediction, e.g. searching for motifs like the splice-site consensus, or on statistical properties such as biased codon usage, etc. (Solovyev et al., 1994; Hebsgaard et al., 1996) have been only partially successful, and investigators have often found that the surest way of predicting a gene is by alignment with a homologous protein sequence (Birney et al., 1996; Gelfand et al., 1996; Huang and Zhang, 1996), or a spliced gene product [an expressed sequence tag (EST), mRNA or cDNA],
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Cited by
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585
Birney, E., Clamp, M., & Durbin, R. (2004) · Genome Research · doi:10.1101/gr.1865504 · Cited by 2,542
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
Wu, T. D., & Watanabe, C. K. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti310 · Cited by 2,354
Metadata
- Authors
- Mott, R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 1997
- Volume
- 13
- Issue
- 4
- Pages
- 477-478
- ISSN
- 0266-7061 (ISSN-L)
- 1367-4803
- 1460-2059
- OpenAlex
- W2112240593
- Cited by
- 276
- References
- 0
- FWCI
- 2.14
- Type
- journal article
- Language
- en
- Open access
- closed
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- Mott, R. (1997). EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Bioinformatics. https://doi.org/10.1093/bioinformatics/13.4.477
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