Putting it Together with Fragment Assembly
Peter Hraber, 7 September 2000
Why?
- To infer tilings from fragments of genomic DNA (e.g., BAC subclones, shotgun fragments)
- To assemble and/or cluster sets of expressed sequence tags
- To create gene indices, or normalized lists of genes
How?
- pairwise sequence similarity
- tuple similarity
- hybrid approaches
- CAVEATS
Exercise
Comparison of assembly techniques:
Do all produce the same result given the same fragments?
- phrap (uses Smith & Waterman) and consed
- TIGR Assembler
- d2_cluster and CRAW
References
- Bouck, J., W. Yu, and K. Worley. 1999. Comparison of gene indexing
databases. Trends in Genetics 15(4):159-162.
- Burke, J., Davison, D., Hide, W. 1999.
d2_cluster: a validated method for clustering EST and full-length cDNA
sequences. Genome Res. 9(11):1135-42.
- Fleischmann, R.D., et al. 1995.
Whole-genome random sequencing and assembly of Haemophilus influenzae
Rd. Science 269:496-512.
- Jongeneel, C.V. 2000.
Searching the expressed sequence tag (EST) databases: panning for genes.
Briefings in Bioinformatics 1(1):76-92.
- Myers, E.W., et al. 2000. A whole-genome assembly of Drosophila.
Science 287:2196-2204.
- Sutton G., White, O., Adams, M., and Kerlavage, A. 1995.
TIGR Assembler: A new tool for assembling large shotgun sequencing
projects. Genome Science & Technology 1:9-19.
Online Resources
- Gene indices
- Assembly Software