Genome Annotation and Curation Using MAKER and MAKER-P

Current Protocols in Bioinformatics

Volumn 2014, Issue , 2014, Pages 4.11.1-4.11.39

  Campbell, Michael S ^a   Holt, Carson ^a,b   Moore, Barry ^a,b   Yandell, Mark ^a,b  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF UTAH   (United States)

Author keywords

Comparative genomics; Gene finding; genome annotation; Plants

Indexed keywords

UNTRANSLATED RNA;

ARTICLE; COMPUTER PROGRAM; GENBANK; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC MODEL; GENOME ANALYSIS; GENOME SIZE; INFORMATION PROCESSING; MEASUREMENT ACCURACY; PREDICTION; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; WEB BROWSER; HUMAN; HUMAN GENOME; SOFTWARE;

GENOME, HUMAN; HUMANS; SOFTWARE;

EID: 84949230870     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi0411s48     Document Type: Article

References (24)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J. D., Amanatides, P. G., and Venter, J.C. 2000. The genome sequence of Drosophila melanogaster. Science 287:2185-2195.
2. Bradnam, K.R., Fass, J.N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J.A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W.C., et al. 2013. Assemblathon 2: Evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2:10. doi:10.1186/2047-217X-2-10.
3. Campbell, M., Law, M., Holt, C., Stein, J., Moghe, G., Hufnagel, D., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C.J., Ware, D., Shiu, S.H., Childs, K.L., Sun, Y., Jiang, N., and Yandell, M. 2013. MAKER-P: A tool-kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 164:513-524.
4. Cantarel, B.L., Korf, I., Robb, S.M.C., Parra, G., Ross, E., Moore, B., Holt, C., Sanchez Alvarado, A., and Yandell, M. 2008. MAKER: An easy-touse annotation pipeline designed for emerging model organism genomes. 18:188-196.
5. Eilbeck, K., Moore, B., Holt, C., and Yandell, M. 2009. Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 10:67.
6. Goff, S.A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A.E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., et al. 2011. The iPlant collaborative: Cyberinfrastructure for plant biology. Front. Plant Sci. 2:34.
7. Holt, C. and Yandell, M. 2011. MAKER2: An annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12:491.
8. Jurka, J., Kapitonov, V.V, Pavlicek, A., Klonowski, P., Kohany, O., andWalichiewicz, J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110:462-467.
9. Korf, I. 2004. Gene finding in novel genomes. BMC Bioinformatics 5:59.
10. Law, M., Childs, K.L., Campbell, M.S., Stein, J.C., Holt, C., Olson, A.J., Holt, C., Lei, J., Jiao, D. Andorf, C.M., Ware, D. Shiu, S.-H., Sun, Y. Jiang, N., and Yandell, M. 2014. Automated update, revision and quality control of the Zeamays genome annotations usingMAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiol. In press.
11. Lévesque, C.A., Brouwer, H., Cano, L., Hamilton, J.P., Holt, C., Huitema, E., Raffaele, S., Robideau, G.P., Thines, M., Win, J., Zerillo, M.M. Beakes, G.W., et al. 2010. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 11:R73.
12. Lipman, D.J. and Pearson, W.R. 1985. Rapid and sensitive protein similarity searches. Science 227:1435-1441.
13. Lowe, T.M. 1999. A computational screen for methylation guide snoRNAs in yeast. Science 283:1168-1171.
14. Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
15. Campbell, M.S., Law, M., Holt, C., Stein, J.C., Moghe, G.D., Hufnagel, D.E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C.J., Ware, D., Shiu, S.H., Childs, K.L., Sun, Y., Jiang, N., and Yandell, M. 2014. MAKER-P: A tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 164:513-524.
16. Neale, D.B., Wegrzyn, J.L., Stevens, K.A., Zimin, A.V., Puiu, D., Crepeau, M.W., Cardeno, C., Koriabine, M., Holtz-Morris, A.E., Liechty, J.D., Martínez-García, P.J., Vasquez-Gross, H.A., et al. 2014. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol. 15:R59.
17. Parra, G., Bradnam, K., andKorf, I. 2007. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061-1067.
18. Press, H., York, N., and Nw, A. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282:2012-2018.
19. Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., and Lopez, R. 2005. InterProScan: Protein domains identifier. Nucleic Acids Res. 33:W116-W120.
20. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S.E., Attwood, J., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
21. Wegrzyn, J.L., Liechty, J.D., Stevens, K.A., Wu, L.-S., Loopstra, C.A., Vasquez-Gross, H.A., Dougherty, W.M., Lin, B.Y., Zieve, J.J., Martínez-García, P.J., Holt, C., Yandell, M., Zimin, A.V., Yorke, J.A., Crepeau, M.W., Puiu, D., Salzberg, S.L., Dejong, P.J., Mockaitis, K., Main, D., Langley, C.H., and Neale, D.B. 2014. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 196:891-909.
22. Yandell, M. and Ence, D. 2012. A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet. 13:329-342.
23. Zimin, A., Stevens, K.A., Crepeau, M.W., Holtz-Morris, A., Koriabine, M., Marçais, G., Puiu, D., Roberts, M., Wegrzyn, J.L., de Jong, P.J., Neale, D.B., Salzberg, S.L., Yorke, J.A., and Langley, C.H. 2014. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics 196:875-890.
24. Zou, C., Lehti-Shiu, M.D., Thibaud-Nissen, F., Prakash, T., Buell, C.R., and Shiu, S.-H. 2009. Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiol. 151:3-15.