The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Fast Computation and Applications of Genome Mappability
Open accessAbstract
We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of massively parallel sequencing experiments. We investigate the properties of the mappability of eukaryotic DNA/RNA both as a whole and at the level of the gene family, providing for various organisms tracks which allow the mappability information to be visually explored. In addition, we show that mappability varies greatly between species and gene classes. Finally, we suggest several practical applications where mappability can be used to refine the analysis of high-throughput sequencing data (SNP calling, gene expression quantification and paired-end experiments). This work highlights mappability as an important concept which deserves to be taken into full account, in particular when massively parallel sequencing technologies are employed. The GEM mappability program belongs to the GEM (GEnome Multitool) suite of programs, which can be freely downloaded for any use from its website (http://gemlibrary.sourceforge.net).
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Alternative isoform regulation in human tissue transcriptomes
Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181
Mobile Elements: Drivers of Genome Evolution
Kazazian, H. H. (2004) · Science · doi:10.1126/science.1089670 · Cited by 1,922
Long Noncoding RNAs with Enhancer-like Function in Human Cells
Ørom, U. A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q., et al. (2010) · Cell · doi:10.1016/j.cell.2010.09.001 · Cited by 1,721
Self-citationEnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., & Birney, E. (2009) · Genome Research · doi:10.1101/gr.073585.107 · Cited by 1,238
A survey of sequence alignment algorithms for next-generation sequencing
Li, H., & Homer, N. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq015 · Cited by 875
Transcriptome genetics using second generation sequencing in a Caucasian population
Montgomery, S. B., Sammeth, M., Gutierrez-Arcelus, M., Lach, R. P., Ingle, C., Nisbett, J., Guigo, R., & Dermitzakis, E. T. (2010) · Nature · doi:10.1038/nature08903 · Cited by 797
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Chow, N. A., Muñoz, J. F., Gade, L., Berkow, E., Li, X., Welsh, R. M., Forsberg, K., Lockhart, S. R., Adam, R., Alanio, A., et al. (2020) · doi:10.1101/2020.01.06.896548 · Cited by 463
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Mapping and characterization of structural variation in 17,795 human genomes
Genomics, N. C. F. C. D., Abel, H. J., Larson, D. E., Regier, A. A., Chiang, C., Das, I., Kanchi, K. L., Layer, R. M., Neale, B. M., Salerno, W. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2371-0 · Cited by 310
Metadata
- Authors
- Derrien, T., Estellé, J., Marco Sola, S., Knowles, D. G., Raineri, E., Guigó, R., & Ribeca, P.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-01-19
- Volume
- 7
- Issue
- 1
- Pages
- e30377
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2018742603
- Cited by
- 487
- References
- 9
- FWCI
- 10.92
- Type
- journal article
- Language
- en
- Open access
- gold
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- Derrien, T., Estellé, J., Marco Sola, S., Knowles, D. G., Raineri, E., Guigó, R., & Ribeca, P. (2012). Fast Computation and Applications of Genome Mappability. PLoS ONE. https://doi.org/10.1371/journal.pone.0030377
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