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Configure Tracks on UCSC Genome Browser: D. ananassae Sep. 2021 (University of Maryland ASM1763931v2/DanaRefSeq2)
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-   Mapping and Sequencing Tracks    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
Assembly Assembly from Fragments
CpG Islands CpG Islands Identified by newcpgreport
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Genes and Gene Prediction Tracks    
RefSeq Genes NCBI RefSeq Genes
D. mel Transcripts BLAT Alignment of D. melanogaster Transcripts
D. mel Proteins Spaln Alignment of D. melanogaster Proteins
genBlastG Genes genBlastG Gene Predictions
GeMoMa Genes GeMoMa Gene Predictions with RNA-Seq
Drosophila RefSeq Transcripts BLAT Alignment of Drosophila RefSeq Transcripts
Potential Frame Shifts Potential Frame Shifts Detected by SPALN2
CDS Mapping TBLASTN Mapping of D. melanogaster CDS
Genscan Genes Genscan Gene Predictions
Geneid Genes Geneid Gene Predictions
N-SCAN N-SCAN Gene Predictions
N-SCAN PASA-EST N-SCAN PASA-EST Gene Predictions
Augustus Augustus Gene Predictions
Augustus (Protein Hints) Augustus Gene Predictions (D. melanogaster Proteins Hints)
GlimmerHMM GlimmerHMM Gene Predictions
InterProScan InterPro Signatures Identified by InterProScan
tRNA Genes Transfer RNA Genes Identified by tRNAscan-SE 2.0
rRNA Genes Ribosomal RNA Genes Identified by RNAmmer
Pfam Conserved Domains Similarity to Pfam Conserved Domains Identified by RPS-BLAST
-   Expression and Regulation    
Combined RAMPAGE TSS Combined RAMPAGE Transcription Start Sites
RAMPAGE TSS Read Density RAMPAGE Read Density for Different Developmental Stages
Combined CSHL RAMPAGE TSS Combined CSHL RAMPAGE Transcription Start Sites
CSHL RAMPAGE TSS Read Density CSHL RAMPAGE Read Density for Different Developmental Stages
CSHL RAMPAGE Alignments CSHL RAMPAGE Read Alignments for Different Developmental Stages
Eye Discs ATAC-Seq ATAC-Seq of D. ananassae Eye Discs
-   RNA-Seq Tracks    
Combined Splice Junctions Combined Splice Junctions for Multiple Developmental Stages and Tissues
RNA-Seq Coverage (Stages) RNA-Seq Coverage for Different Developmental Stages
RNA-Seq Coverage (Tissues) RNA-Seq Coverage for Different Tissues
TransDecoder Transcripts Transcripts and Coding Regions Predicted by TransDecoder
Trinity Transcripts Transcripts Assembled by Genome-Guided Trinity
-   PacBio Iso-Seq Tracks    
FLNC Iso-Seq Reads Alignments of Full-Length Non-Chimeric (FLNC) Iso-Seq Reads
Clustered Iso-Seq Reads Alignments of Clustered Iso-Seq Reads
Collapsed Iso-Seq Transcripts Non-redundant Transcripts Derived from Clustered Iso-Seq Reads
SQANTI3 QC Transcripts Iso-Seq Transcripts Classified by SQANTI3 QC
SQANTI3 Filtered Transcripts Iso-Seq Transcripts Filtered by SQANTI3 Using the Default Rules
uLTRA FLNC Iso-Seq Reads uLTRA Alignments of Full-Length Non-Chimeric (FLNC) Iso-Seq Reads
uLTRA Collapsed Iso-Seq Transcripts Non-redundant Transcripts Derived from uLTRA Alignments of Iso-Seq Reads
TAMA Collapsed Transcripts Iso-Seq Transcripts Assembled by TAMA Collapse
StringTie2 Iso-Seq Transcripts Transcripts Assembled by StringTie2 Using PacBio Iso-Seq Reads
Scallop-LR Iso-Seq Transcripts Transcripts Assembled by Scallop-LR Using PacBio Iso-Seq Reads
TransDecoder Iso-Seq Transcripts Transcripts Predicted by TransDecoder Using PacBio Iso-Seq and Illumina RNA-Seq Reads
-   Comparative Genomics    
D. melanogaster Chain D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Chained Alignments
D. melanogaster Net D. melanogaster (Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)) Alignment Net
D. ananassae DanaCAF1 Chain D. ananassae (May 2011 (Agencourt dana_caf1/DanaCAF1)) Chained Alignments
D. ananassae DanaCAF1 Net D. ananassae (May 2011 (Agencourt dana_caf1/DanaCAF1)) Alignment Net
-   Variation and Repeats    
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust
RepeatMasker Repeating Elements by RepeatMasker
TE Density RepeatMasker Transposon Density (1kb window, 100bp step size)
TANTAN Simple Repeats Identified by TANTAN
TANTAN Tandem Tandem Repeats Identified by TANTAN
RepeatModeler Transposons Identified by RepeatModeler
TransposonPSI (Pfam) Pfam Transposon Protein Domains Identified by TransposonPSI