Additional file 6

By Dimas Yusuf, S. Butland, Magdalena I. Swanson, Eugene Bolotin, Amy Ticoll, Warren A. Cheung, X. Zhang, C. T. Dickman, Debra L. Fulton, Jonathan S. Lim and 104 more. 2009

1,989 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/09ef66adbc7cfa3356f5996c8bc01ca2506d379b

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Citations in the corpus

Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis (2012, methodology): “To assess representation of the complete tomato transcriptome, contigs (GA2- and Sanger-derived) were aligned with the Heinz 1706 Tomato Genome Initiative (TGI) gene model set (version iTAG2; ITAG, 2011) using Exonerate (Slater and Birney, 2005).”
Interactive machine learning for health informatics: when do we need the human-in-the-loop? (2016, unknown): “For more details refer to [32].”
GENCODE: The reference human genome annotation for The ENCODE Project (2012, methodology): “(cid:129) CExonic is a locally developed method that uses exonerate (Slater and Birney 2005) to align mouse and human transcripts and then looks for patterns of conservation in exonic structure.”
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm (2012, unknown): “These heuristics perform Exonerate local alignments (Slater and Birney, 2005) between the 5000 query sequences and 999 target sequences, the latter including extant sequences from the reference alignment and PAGAN-inferred ancestral sequences.”
A draft human pangenome reference (2022, methodology): “The missing genes were then attempted to be mapped to these regions using an identical process as described above for the initial mappings, involving MAFFT, minimap2 and Exonerate.”
Using Tablet for visual exploration of second-generation sequencing data (2013, background): “The tooltip can adapt its display to the assembly format in use (Figure 2), providing additional information if the reads contain CIGAR [10] entries, or in the case of paired data where mate position, inferred insert size and a twin tooltip containing the mate’s information can then be shown.”
Predicting Genes in Single Genomes with AUGUSTUS (2018, methodology): “In general, there are tools that produce alignments with a high specificity at the expense of sensitivity (e.g., GenomeThreader; Gremme, 2013) and more sensitive but less specific tools (e.g., Exonerate; Slater & Birney, 2005).”
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology (2008, background): “Currently, Exonerate (Slater and Birney, 2005) and Eland (Illumina Inc.”