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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...and 5 kb (Colby and Williams 1993). The 5-kb repeat unit has a 242-bp insert between H1 and H3 genes. These variants are present in a number of Drosophila species, indicating that their origin predates the speciation event (Strausbaugh and Weinberg 1982). Figure 3B shows the distribution of 5- and 4...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...-derived sequences (Lipatov et al. 2005). A recent transcriptome-wide study identified 327 genes in Drosophila melanogaster that generate chimeric transcripts across different populations (Oliveira et al. 2023). Among all genes, 76 generate chimeric transcripts from TE insertions that were present in one strain...
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12 Drosophila Genomes/Letter: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- Michael F. Lin,
- Joseph W. Carlson,
- Madeline A. Crosby,
- Beverley B. Matthews,
- Charles Yu,
- Soo Park,
- Kenneth H. Wan,
- Andrew J. Schroeder,
- L. Sian Gramates,
- Susan E. St. Pierre,
- Margaret Roark,
- Kenneth L. Wiley, Jr.,
- Rob J. Kulathinal,
- Peili Zhang,
- Kyl V. Myrick,
- Jerry V. Antone,
- Susan E. Celniker,
- William M. Gelbart,
- and Manolis Kellis
Genome Res. December 2007 17: 1823-1836; Published in Advance November 7, 2007, doi:10.1101/gr.6679507
...Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes Michael F. Lin 1 , Joseph W. Carlson 2 , Madeline A. Crosby 3 , Beverley B. Matthews 3 , Charles Yu 2 , Soo Park 2 , Kenneth H. Wan 2...
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METHODS: Ab initio Gene Finding in Drosophila Genomic DNA
- Asaf A. Salamov and
- Victor V. Solovyev
Genome Res. April 1, 2000 10: 516-522; doi:10.1101/gr.10.4.516
...Ab initio Gene Finding in Drosophila Genomic DNA Asaf A. Salamov and Victor V. Solovyev 1 The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Abstract Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained...
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LETTER: Evaluation of Gene-Finding Programs on Mammalian Sequences
- Sanja Rogic,
- Alan K. Mackworth,
- and Francis B.F. Ouellette
Genome Res. May 1, 2001 11: 817-832; doi:10.1101/gr.147901
...of British Columbia, Vancouver, BC V6T 1Z4, Canada; 3Centre for Molecular Medicine and Therapeutics, Vancouver, BC V5Z 4H4, Canada Abstract We present an independent comparative analysis of seven recently developed gene-finding programs: FGENES , GeneMark.hmm , Genie , Genscan , HMMgene , Morgan , and MZEF...
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LETTER: Genome Annotation Assessment in Drosophila melanogaster
- Martin G. Reese,
- George Hartzell,
- Nomi L. Harris,
- Uwe Ohler,
- Josep F. Abril,
- and Suzanna E. Lewis
Genome Res. April 1, 2000 10: 483-501; doi:10.1101/gr.10.4.483
.... Of these 222 gene structures, 182 are similar to a homologous protein in another organism or have a Drosophila EST hit. For these structures, the intron–exon boundaries were verified by partial cDNA/EST alignments using sim4 ( Florea et al. 1998 ), homologies were discovered using BLASTX , TBLASTX , and PFAM...
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LETTER: Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis
- Justen Andrews,
- Gerard G. Bouffard,
- Chris Cheadle,
- Jining Lü,
- Kevin G. Becker,
- and Brian Oliver
Genome Res. December 1, 2000 10: 2030-2043; doi:10.1101/gr.159800
...Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis Justen Andrews 1 , Gerard G. Bouffard 2 , Chris Cheadle 3 , Jining Lü 1 , Kevin G. Becker 3 , and Brian Oliver 1 , 4...
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METHODS: SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model
- Marina Alexandersson,
- Simon Cawley,
- and Lior Pachter
Genome Res. March 1, 2003 13: 496-502; Published in Advance February 12, 2003, doi:10.1101/gr.424203
.... , Krauss R.M. , Rubin E.M. ( 2001 ) An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science 294 : 169 – 173 . ↵ Reese M.G. , Kulp D. , Tammana H. , Haussler D. ( 2000 ) Genie—Gene finding in Drosophila melanogaster. Genet. Res. 10 : 529 – 538 . ↵ Wiehe T...
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Research: Evidence of abundant stop codon readthrough in Drosophila and other metazoa
- Irwin Jungreis,
- Michael F. Lin,
- Rebecca Spokony,
- Clara S. Chan,
- Nicolas Negre,
- Alec Victorsen,
- Kevin P. White,
- and Manolis Kellis
Genome Res. December 2011 21: 2096-2113; Published in Advance October 12, 2011, doi:10.1101/gr.119974.110
...using only the six closest relatives of D. melanogaster (up to and including Drosophila ananassae). Using our frame bias test to infer the number of Figure 6. RNA structures associated with readthrough genes. (A) Fly, human, andworm examples of conserved, stable RNA structures predicted...
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METHODS: GeneID in Drosophila
- Genís Parra,
- Enrique Blanco,
- and Roderic Guigó
Genome Res. April 1, 2000 10: 511-515; doi:10.1101/gr.10.4.511
...for sites, and the Markov model of coding DNA in Drosophila melanogaster . We also compare other models of coding DNA with the Markov model. Finally, we present and discuss the results obtained when GeneID is used to predict genes in the Adh region. These results show that the accuracy of Gene...

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