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Configure Tracks on UCSC Genome Browser: D. kikkawai July 2022 (GEP/DkikHiC1)
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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
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Genes and Gene Prediction Tracks    
RefSeq Genes BLAT Alignments of 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
tRNA Genes Transfer RNA Genes Identified by tRNAscan-SE 2.0
rRNA Genes Ribosomal RNA Genes Identified by RNAmmer
BUSCO (diptera_odb10) BUSCO Genes from the diptera_odb10 Dataset
Pfam Conserved Domains Similarity to Pfam Conserved Domains Identified by RPS-BLAST
D. kik Mitochondria Sequence Similarity to D. kikkawai Mitochondria Genome
Wolbachia Endosymbionts Megablast Alignments to Wolbachia Endosymbionts
-   Expression and Regulation    
Combined CSHL RAMPAGE TSS Combined CSHL RAMPAGE Transcription Start Sites
CSHL RAMPAGE TSS Read Density CSHL RAMPAGE Read Density for Different Developmental Stages
-   RNA-Seq Tracks    
Combined Splice Junctions Combined Splice Junctions for Multiple Developmental Stages
RNA-Seq Coverage (Stages) RNA-Seq Coverage for Different Developmental Stages
TransDecoder Transcripts Transcripts and Coding Regions Predicted by TransDecoder
Trinity Transcripts Transcripts Assembled by Genome-Guided Trinity
-   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. kikkawai DkikGB2 Chain D. kikkawai (Apr. 2013 (BCM-HGSC/Dkik_2.0)) Chained Alignments
D. kikkawai DkikGB2 Net D. kikkawai (Apr. 2013 (BCM-HGSC/Dkik_2.0)) Alignment Net
D. kikkawai DkikPurged1 Chain D. kikkawai (Dec. 2020 (GEP/DkikPurged1)) Chained Alignments
D. kikkawai DkikPurged1 Net D. kikkawai (Dec. 2020 (GEP/DkikPurged1)) 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
EDTA Intact Repeats Intact Repeats Identified by EDTA
EDTA TEanno Repeats Intact and Fragmented Repeats Identified by EDTA (TEanno)
Octopus Variants Variants Identified by Octopus
Inspector Small Errors Small-Scale Errors Identified by Inspector
Inspector Structural Errors Structural Errors Identified by Inspector