Projects
Comparative Genomic Sequence Data in Drosophila
- Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Casey M. Bergman, Barret D. Peiffer, Diego Rincon-Limas, Roger A. Hoskins, Andreas Gnirke, Chris J. Mungall, Adrienne M. Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A. George, Pieter J. De Jong, Juan Botas, Gerald M. Rubin and Susan E. Celniker
Thank you for your interest in our pilot study on sequence conservation in candidate regions from select species in the genus Drosophila. The following data were used as the basis for our publication in Genome Biology. These data will not be updated.
Any questions should be directed to Sue Celniker: celniker@fruitfly.org
| Annotated fosmid sequences from Drosophila species. |
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The following 30 fosmids were isolated, sequenced and annotated as described in Bergman, et al. (2002) Genome Biology 3:0086, and are avaible here in GenBank or GAME-XML format. XML files can be viewed using the Apollo genome annnotation and curation tool. The fosmid libraries from which these clones were isolated are described and are available through BacPac resources. The strains from which these libraries were made are available through the Tucson Drosophila. Species Stock Center. Note that some of the XML files and archives are large, so it is advisable to use the "save link as" option in your browser. |
| Genomic Region | D. erecta | D. pseudoobscura | D. willistoni | D. virilis* (was thought to be D. littoralis) |
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| Rhodopsin 1 (ninaE) | Genbank XML | Genbank XML | Genbank XML | Genbank XML |
| Rhodopsin 2 (Rh2) | Genbank XML | Genbank XML | Genbank XML | Genbank XML |
| Rhodopsin 3 (Rh3) | Genbank XML | Genbank XML | Genbank XML | Genbank XML |
| Rhodopsin 4 (Rh4) | Genbank XML | Genbank XML | Genbank XML | Genbank XML |
| apterous (ap) | Genbank XML | Genbank XML | Genbank XML | Genbank XML |
| even-skipped (eve) | Genbank XML | Genbank XML | Genbank XML | Genbank XML |
| fushi-tarazu (ftz) | Genbank XML | Genbank XML | N.A. | Genbank XML |
| twist (twi) | Genbank XML | Genbank XML | N.A. | Genbank XML |
During the initial phases of this project, a P1 clone from the D. virilis ap region was also obtained: Genbank XML
An archive of the unannotated FASTA sequence files can be found here.
An archive of the GAME-XML annotated sequence files can be found here.
Coding sequence alignments used for Ka/Ks analyses in FASTA Format: amino acid alignments coding sequence alignments
Release 3 sequences and annotations of D. melanogaster region corresponding to union of homologous fosmid sequences: FASTA genomic sequences VISTA format annotations
Links to Drosophila pseudoobscura comparative genomic resources.
The Human Genome Sequencing Center (HGSC) at Baylor College of Medecine is currently sequencing the genome of Drosophila pseudoobscura, providing a critical resource for the whole-genome comparative analyses in the genus Drosophila. Updates on the status of sequences and assemblies, ftp repositories, information concerning the use of this data, and a BLAST server can be found on Baylor's HGSC website.
Inna Dubchak's group at Lawrence Berkeley National Laboratory has produced a preliminary whole-genome alignment of the January 2003 Baylor assembly which can be accessed using the VISTA genome browser.