References#
The following publications correspond to third-party software used by Ensembl Anno.
Hazem Z. Girgis. Red: an intelligent, rapid, accurate tool for detecting repeats de novo on the genomic scale. BMC Bioinformatics, 16:227, 2015. doi:10.1186/s12859-015-0654-5.
Gary Benson. Tandem repeats finder: a program to analyze dna sequences. Nucleic Acids Research, 27(2):573–580, 1999. doi:10.1093/nar/27.2.573.
A. F. A. Smit, R. Hubley, and P. Green. Repeatmasker open-4.0. 2013. URL: http://www.repeatmasker.org.
R. V. Davuluri, I. Grosse, and M. Q. Zhang. Computational identification of promoters and first exons in the human genome. Nature Genetics, 29(4):412–417, 2001. doi:10.1038/ng769.
Thomas A. Down and Tim J. P. Hubbard. Computational detection and location of transcription start sites in mammalian genomic dna. Genome Research, 12(3):458–461, 2002. doi:10.1101/gr.216902.
Eric P. Nawrocki, David L. Kolbe, and Sean R. Eddy. Infernal 1.0: inference of rna alignments. Bioinformatics, 25(10):1335–1337, 2009. doi:10.1093/bioinformatics/btp157.
Todd M. Lowe and Sean R. Eddy. Trnascan-se: a program for improved detection of transfer rna genes in genomic sequence. Nucleic Acids Research, 25(5):955–964, 1997. doi:10.1093/nar/25.5.955.
Alexander Dobin, Carrie A. Davis, Felix Schlesinger, and others. Star: ultrafast universal rna-seq aligner. Bioinformatics, 29(1):15–21, 2013. doi:10.1093/bioinformatics/bts635.
Mihaela Pertea, Geo M. Pertea, Christine M. Antonescu, Tsung-Cheng Chang, Joshua T. Mendell, and Steven L. Salzberg. Stringtie enables improved reconstruction of a transcriptome from rna-seq reads. Nature Biotechnology, 33(3):290–295, 2015. doi:10.1038/nbt.3122.
Mingfu Shao and Carl Kingsford. Accurate assembly of transcripts through phase-preserving graph decomposition. Nature Biotechnology, 35(12):1167–1169, 2017. doi:10.1038/nbt.4020.
Heng Li. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18):3094–3100, 2018. doi:10.1093/bioinformatics/bty191.
Rui She, Justin S. C. Chu, Kai Wang, Jian Pei, and Nanjiang Chen. Genblasta: enabling blast to identify homologous gene sequences. Genome Research, 19(1):143–149, 2009. doi:10.1101/gr.082081.108.
Heng Li. Miniprot: a tool for protein-to-genome alignment. Bioinformatics, 39(1):btad014, 2023. doi:10.1093/bioinformatics/btad014.