References
Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., … Venter, J. C. (2000). The genome sequence of Drosophila melanogaster . Science ,287 (5461), 2185–95. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/10731132
Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research ,25 (17), 3389–3402. doi:10.1093/nar/25.17.3389
Clifton, B. D., Librado, P., Yeh, S.-D., Solares, E. S., Real, D. A., Jayasekera, S. U., … Ranz, J. M. (2017). Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila . Molecular Biology and Evolution , 34 (1), 51–65. doi:10.1093/molbev/msw212
Dominguez Del Angel, V., Hjerde, E., Sterck, L., Capella-Gutierrez, S., Notredame, C., Vinnere Pettersson, O., … Lantz, H. (2018). Ten steps to get started in Genome Assembly and Annotation.F1000Research , 7 , ELIXIR-148. doi:10.12688/f1000research.13598.1
Eddy, S. R. (2011). Accelerated Profile HMM Searches. PLoS Computational Biology , 7 (10), e1002195. doi:10.1371/journal.pcbi.1002195
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., … Punta, M. (2014). Pfam: the protein families database. Nucleic Acids Research , 42 (Database issue), D222–D230. doi:10.1093/nar/gkt1223
Gremme, G., Brendel, V., Sparks, M. E., & Kurtz, S. (2005). Engineering a software tool for gene structure prediction in higher organisms.Information and Software Technology , 47 (15), 965–978. doi:10.1016/J.INFSOF.2005.09.005
Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M., & Stanke, M. (2016). BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinformatics , 32 (5), 767–769. doi:10.1093/bioinformatics/btv661
Holt, C., & Yandell, M. (2011). MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.BMC Bioinformatics , 12 (1), 491. doi:10.1186/1471-2105-12-491
Joseph, R. M., & Carlson, J. R. (2015). DrosophilaChemoreceptors: A Molecular Interface Between the Chemical World and the Brain. Trends in Genetics : TIG , 31 (12), 683–695. doi:10.1016/j.tig.2015.09.005
Keilwagen, J., Hartung, F., & Grau, J. (2019). GeMoMa: Homology-based gene prediction utilizing intron position conservation and RNA-seq data. In Methods in Molecular Biology (Vol. 1962, pp. 161–177). Humana Press Inc. doi:10.1007/978-1-4939-9173-0_9
Keilwagen, J., Hartung, F., Paulini, M., Twardziok, S. O., & Grau, J. (2018). Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC Bioinformatics , 19 (1), 189. doi:10.1186/s12859-018-2203-5
Keilwagen, J., Wenk, M., Erickson, J. L., Schattat, M. H., Grau, J., & Hartung, F. (2016). Using intron position conservation for homology-based gene prediction. Nucleic Acids Research ,44 (9), 89. doi:10.1093/nar/gkw092
Keller, O., Kollmar, M., Stanke, M., & Waack, S. (2011a). A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics , 27 (6), 757–763. doi:10.1093/bioinformatics/btr010
Keller, O., Kollmar, M., Stanke, M., & Waack, S. (2011b). A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics , 27 (6), 757–763. doi:10.1093/bioinformatics/btr010
Korf, I. (2004). Gene finding in novel genomes. BMC Bioinformatics , 5 , 59. doi:10.1186/1471-2105-5-59
Lee, E., Helt, G. A., Reese, J. T., Munoz-Torres, M. C., Childers, C. P., Buels, R. M., … Lewis, S. E. (2013). Web Apollo: a web-based genomic annotation editing platform. Genome Biology ,14 (8), R93. doi:10.1186/gb-2013-14-8-r93
Lomsadze, A., Burns, P. D., & Borodovsky, M. (2014). Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic Acids Research , 42 (15), e119–e119. doi:10.1093/nar/gku557
Pelosi, P., Iovinella, I., Felicioli, A., & Dani, F. R. (2014). Soluble proteins of chemical communication: an overview across arthropods.Frontiers in Physiology , 5 (August), 320. doi:10.3389/fphys.2014.00320
Robertson, H. M. (2015). The Insect Chemoreceptor Superfamily Is Ancient in Animals. Chemical Senses , 40 (9), 609–614. doi:10.1093/chemse/bjv046
Sánchez-Herrero, J. F., Frías-López, C., Escuer, P., Hinojosa-Alvarez, S., Arnedo, M. A., Sánchez-Gracia, A., & Rozas, J. (2019). The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates. GigaScience 8 (8), 1-9. doi:10.1093/gigascience/giz099
Slater, G. S. C., & Birney, E. (2005). Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics , 6 , 31. doi:10.1186/1471-2105-6-31
Stanke, M., & Waack, S. (2003). Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics , 19 (Suppl 2), ii215–ii225. doi:10.1093/bioinformatics/btg1080
Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics , 24 (5), 637–644. doi:10.1093/bioinformatics/btn013
Stanke, M., Schöffmann, O., Morgenstern, B., & Waack, S. (2006). Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics ,7 (1), 62. doi:10.1186/1471-2105-7-62
Vieira, F. G., Sánchez-Gracia, A., & Rozas, J. (2007). Comparative genomic analysis of the odorant-binding protein family in 12Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biology , 8 (11), R235. doi:10.1186/gb-2007-8-11-r235
Vizueta, J., Frías-López, C., Macías-Hernández, N., Arnedo, M. A., Sánchez-Gracia, A., & Rozas, J. (2017). Evolution of chemosensory gene families in arthropods: Insight from the first inclusive comparative transcriptome analysis across spider appendages. Genome Biology and Evolution , 9 (1), 178–196. doi:10.1093/gbe/evw296
Vizueta, J., Rozas, J., & Sánchez-Gracia, A. (2018). Comparative Genomics Reveals Thousands of Novel Chemosensory Genes and Massive Changes in Chemoreceptor Repertories across Chelicerates. Genome Biology and Evolution , 10 (5), 1221–1236. doi:10.1093/gbe/evy081
Yandell, M., & Ence, D. (2012). A beginner’s guide to eukaryotic genome annotation. Nature Reviews Genetics , 13 (5), 329–342. doi:10.1038/nrg3174
Yohe, L. R., Davies, K. T. J., Simmons, N. B., Sears, K. E., Dumont, E. R., Rossiter, S. J., & Dávalos, L. M. (2019). Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family.Molecular Ecology Resources . doi:10.1111/1755-0998.13093
Zhang, Y., Zheng, Y., Li, D., & Fan, Y. (2014). Transcriptomics and identification of the chemoreceptor superfamily of the pupal parasitoid of the oriental fruit fly, Spalangia endius Walker (Hymenoptera: Pteromalidae). PloS One , 9 (2), e87800. doi:10.1371/journal.pone.0087800