--------------------------------------------------------------- balAcu1.trackDb.html : Differences exist between hgwbeta and hgw2 (RR fields taken from public MySql server, not individual machine) 724c724 < nestedRepeats | from the output of the --- > nestedRepeats | from the output of the 787,788c787,788 < nestedRepeats | < nestedRepeats | https://www.repeatmasker.org/. 1996-2010. --- > nestedRepeats | > nestedRepeats | http://www.repeatmasker.org. 1996-2010. 847c847 < refSeqComposite | hide. Note: Not all subtracks are available on all assemblies.

--- > refSeqComposite | hide. Note: Not all subtracts are available on all assemblies.

901,921d900 < refSeqComposite |

< refSeqComposite | NCBI Orthologs – Orthologous genes were identified by < refSeqComposite | < refSeqComposite | NCBI's Eukaryotic Genome Annotation Pipeline < refSeqComposite | for the NCBI Gene dataset using a combination of protein sequence similarity < refSeqComposite | and local synteny analysis. Orthology is determined between the genome being annotated and a < refSeqComposite | reference genome, such as human or zebrafish, and pairs of orthologs are grouped together. < refSeqComposite | Transitive relationships are inferred within each group, for example, zebrafish <-> < refSeqComposite | human <-> mouse. For more information on how NCBI calculates orthologs, see the details < refSeqComposite | provided < refSeqComposite | < refSeqComposite | here. This track is available for the following assemblies: < refSeqComposite | hg38, < refSeqComposite | mm39, < refSeqComposite | danRer11, < refSeqComposite | canFam6, and < refSeqComposite | bosTau9. < refSeqComposite |

1033,1044d1011 < refSeqComposite |

< refSeqComposite | The NCBI Orthologs track was generated using the latest < refSeqComposite | NCBI files (gene2accession and < refSeqComposite | gene_orthologs). NCBI chromosome identifiers were mapped to UCSC-compatible IDs using < refSeqComposite | species-specific chromosome alias files, and genes were filtered to include only those located on < refSeqComposite | valid NCBI chromosomes. A custom Python script processed the ortholog relationships and created bed files for < refSeqComposite | each species. The bed files were then converted to BigBed format, with indexing for search < refSeqComposite | functionality. The procedure is documented in the makeDoc from our GitHub repository.

1062c1029 < refSeqComposite | The data in the RefSeq Other, RefSeq Diffs, and NCBI Orthologs tracks are organized in --- > refSeqComposite | The data in the RefSeq Other and RefSeq Diffs tracks are organized in 1085c1052 < refSeqComposite | The annotations in the RefSeqOther, RefSeqDiffs, and NCBI Orthologs tracks are stored in bigBed --- > refSeqComposite | The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed 1088,1092c1055,1057 < refSeqComposite | target="_blank">ncbiRefSeqOther.bb, < refSeqComposite | ncbiRefSeqDiffs.bb, and < refSeqComposite | ncbiOrtho.bb. --- > refSeqComposite | target="_blank">ncbiRefSeqOther.bb and > refSeqComposite | refSeqComposite | target="_blank">ncbiRefSeqDiffs.bb. 1162c1127 < rmsk | RepeatMasker --- > rmsk | RepeatMasker 1181,1193d1145 < rmsk |

< rmsk | When analyzing the data tables of this track, keep in mind that Repbase is not the same < rmsk | as the Repeatmasker sequence database and that the repeat names in the < rmsk | Repeatmasker output are not the same as the sequence names in the Repeatmasker < rmsk | database. Concretely, you can find a name such as "L1PA4" in the Repeatmasker < rmsk | output and this track, but there is not necessarily a single sequence "L1PA4" < rmsk | in the Repeatmasker database. This is because Repeatmasker creates annotations < rmsk | by joining matches to partial pieces of the database together so there is no < rmsk | 1:1 relationship between its sequence database and the annotations. To learn < rmsk | more, you can read the Repeatmasker paper, its source code or reach out to the < rmsk | Repeatmasker authors, your local expert on transposable elements or us. < rmsk |

--- > uniprot | In the "UniProt Modifications" track, lipoification sites are highlighted in > uniprot | dark blue, glycosylation sites in > uniprot | dark green, and phosphorylation in > uniprot | light green.