Data

The manually annotated corpus of species mentions from Gerner et al (2010) can be found at the project sourceforge page.

Coordinates of TE/Repeat predictions from BLASTER, ReAS, CompTE, and RepeatRunner for 12 species in the genus Drosophila from Clark et al. (2007) can be found here.

Coordinates of noncoding RNA gene predictions for 12 species in the genus Drosophila from Clark et al. (2007) can be found here.

Coordinates of nuclear tRNA gene predictions for 12 species in the genus Drosophila from Clark et al. (2007) can be found here. These gene predictions are derived from the union of tRNAscan-SE 1.23 and aragorn 1.1 and subsequently parsed by the TFAM 0.02 classfier to confirm tRNA identities and predict initiator tRNA genes.

Polymorphism and divergence alignments of D. melanogaster noncoding regions from Casillas et al. (2007) are available here.

Alignments 27 LTR and 19 non-LTR D. melanogaster retrotransposon families from Bergman and Bensasson (2007) are available here.

120 promoter motifs from Down et al. (2007) can be browsed at Thomas Down‘s Tiffin database. Text files of .xms formatted PWMs from Down et al. (2007) can be found here for Supplemental File 1 (120 motifs inferred from D. melanogaster 5′ flanking sequences), Supplemental File 2, (30 motifs inferred from DNAse I footprints), and Supplemental File 3 (172 motifs from JASPAR CORE and additional SELEX evidence). Further information about 57 Drosophila transcription factor motifs curated from the literature used in Down et al. (2007) can be found here.

Datasets from Pierstorff et al. (2006) can be found at Nora Pierstorff’s homepage.

Coordinates of natural transposable elements in the Release 4 genome sequence from Quesneville et al. (2005) can be found at FlyBase’s Genome Annotation ftp site.

The Drosophila DNase I footprint database – a systematic genome annotation of over 1,350 transcription factor binding sites in D. melanogaster – from Bergman et al. (2005) can be found at www.flyreg.org. As of October 2007, the Drosophila DNAse I footprint database has fully merged with the REDfly database to provide a one-stop portal for cis-regulatory data in Drosophila.

Simulated noncoding sequences and alignments from Pollard et al. (2004) can be found at the Eisen Lab’s Alignment Benchmarking page.

Sequences, annotations and alignments from Bergman et al. (2002) can be found on the BDGP’s Comparative Genomics page.

Sequences, annotations and alignments of natural transposable elements in Release 3 from Kaminker et al. (2002) can be found on the BDGP’s Natural Transposable Element page and from FlyBase’s Genome Annotation ftp site.

Sequence data for D. melanogasterD. virilis orthologous noncoding regions analyzed in Bergman & Kreitman (2001), Emberly et al. (2003) and Sinha & Siggia (2005) can be found here [Note: save to file, this file loads poorly in some browsers]. The conserved noncoding sequences identified in Bergman & Kreitman (2001) can be found as supplementary material on the Genome Research web site.

Binding site data used in Ludwig et al. (2000), Berman et al. (2002), Dermitzakis et al. (2003) and Phinchongsakuldit et al. (2004) can be found here (bcd, hb, or Kr). Up-to-date, expanded versions of these data sets can be found at www.flyreg.org. The position weight matrices (PWMs) used in Ludwig et al. (2000) can be found in my thesis.

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