--------------------------------------------------------------- ce11.trackDb.html : Differences exist between hgwbeta and hgw2 (RR fields taken from public MySql server, not individual machine) 366c366 < chainSelf | RepeatMasker --- > chainSelf | RepeatMasker 1476c1476 < cons135way | cons135way | cons26way | crispr | algorithms through the tool Crispor downloads page, which --- > crispr | href="http://crispor.tefor.net/downloads/">Crispor downloads page, which 2680c2680 < crisprRanges | algorithms through the tool crisprRanges | algorithms through the tool Crispor downloads page, which --- > crisprRanges | href="http://crispor.tefor.net/downloads/">Crispor downloads page, which 2897c2897 < crisprTargets | algorithms through the tool crisprTargets | algorithms through the tool Crispor downloads page, which --- > crisprTargets | href="http://crispor.tefor.net/downloads/">Crispor downloads page, which 3782,3786c3782,3787 < nematodesChainNet |
< nematodesChainNet | LASTZ was developed at < nematodesChainNet | Miller Lab at Pennsylvania State University by < nematodesChainNet | Bob Harris. < nematodesChainNet |
--- > nematodesChainNet |> nematodesChainNet | Lastz (previously known as blastz) was developed at > nematodesChainNet | nematodesChainNet | TARGET=_blank>Pennsylvania State University by > nematodesChainNet | Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from > nematodesChainNet | Ross Hardison.
3789c3790 < nematodesChainNet | RepeatMasker --- > nematodesChainNet | RepeatMasker 3805,3811d3805 < nematodesChainNet |< nematodesChainNet | Harris RS. < nematodesChainNet | Improved pairwise alignment of genomic DNA. < nematodesChainNet | Ph.D. Thesis. Pennsylvania State University, USA. 2007. < nematodesChainNet |
< nematodesChainNet | 3849c3843 < nestedRepeats | from the output of the --- > nestedRepeats | from the output of the 3912,3913c3906,3907 < nestedRepeats | < nestedRepeats | https://www.repeatmasker.org/. 1996-2010. --- > nestedRepeats | > nestedRepeats | http://www.repeatmasker.org. 1996-2010. 4113c4107 < refSeqComposite | hide. Note: Not all subtracks are available on all assemblies. --- > refSeqComposite | hide. Note: Not all subtracts are available on all assemblies. 4167,4187d4160 < 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.
4328c4289 < 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 4351c4312 < 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 4354,4358c4315,4317 < refSeqComposite | target="_blank">ncbiRefSeqOther.bb, < refSeqComposite | ncbiRefSeqDiffs.bb, and < refSeqComposite | ncbiOrtho.bb. --- > refSeqComposite | target="_blank">ncbiRefSeqOther.bb and > refSeqComposite | refSeqComposite | target="_blank">ncbiRefSeqDiffs.bb. 4427c4386 < rmsk | HREF="https://www.repeatmasker.org/" --- > rmsk | HREF="http://www.repeatmasker.org/" 4816,4821c4775,4778 < uniprot | Features in the "UniProt Modifications" (modified residues) track are drawn in < uniprot | light green. Disulfide bonds are shown in < uniprot | dark grey. Topological domains < uniprot | in maroon and zinc finger regions in < uniprot | olive green. < uniprot | --- > 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.