about the Segmental Duplications track. The > track shows regions of the genome that appear in two or more copies with > ≥90% identity and ≥1kb in length. > > For your specific

Thanks for this, Max. I recently exchanged email with a researcher in Diethard Tautz' lab regarding work they have been doing on the Mus spicilegus

terms "segmental duplications" and "pseudogenes": - https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=segmental%20duplications - https

in our Segmental Duplications track that shows regions of the genome with over 90% similar: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=genomicSuperDups. You

regions or segmental duplications, which occur throughout the genome and are often found on multiple chromosomes. LiftOver chain files are created by first aligning the entire genome

which have segmental duplications (as can be seen via BLAT). This > leads to some ambiguity inherent in gene annotations; NCBI Refseq, Ensembl, > and UCSC each call the "

> > Hello, > > I am writing to ask if the team running the UCSG genome browser would please consider posting the MacaM genome sequence from

part of segmental duplications in hg19, like the example you provided, it's not uncommon for reciprocal alignments to get confused about which is the most homologous when going

Hi, I am one of the Clinical Analysts at the Division of Genomic Diagnostics and also responsible for clinical pipeline operations involving SNP Arrays

than lifting segmental duplications, which is not a very guaranteed outcome, they should rather be recomputed. Here are some outlined ideas that could provide a scripting solution

supporting the segmental duplications track data. You can read the segmental duplications track description page for information on how the track was produced. http://genome.

a "Segmental Duplications" track for the dog/canFam3 assembly. We do not have a "Segmental Duplications" track for the canFam3 assembly. The data for these

genome] Segmental Duplications in GRCh38 Dear Luvina, Thank you for your reply. I had read the documentation page you linked, but the information it contains appears to be incorrect

in the Segmental Dups track. Information about the orientation of individual duplication sites can be found by clicking on the site in the browser. On the resulting page, the value

Good morning, I am comparing two genomes using the UCSC pipeline : Latsz + axtChain + chainNet. I

of a segmental duplication that maps to the other U2AF1 location on chr21. In the following session, you can see the newly added contig at the top in red, the U2AF1 transcripts in various

Dear UCSC team, I needed to update the chromosomal positions on 2896684 SNPs distributed all over the

Hello, I want to extract regions with sequence identity of 95% to another genomic region based on

in the segmental duplications track are also marked by the self chain track. 128 of the segmental duplication records (out of roughly 50 thousand) have no overlap with self chains,

can download Segmental Duplications (hg19, Repeats, Segmental Dups), and it is very clear that, in the same row, I can see the sequence position of the first duplication and the position

Hi While using the in silico PCR or Blat Tool I use the GRCh37/hg19 human reference assembly. Is

In the March 2006 assembly, there are some BACs that appear to be much larger than expected. For

Hello, I am interested in the frequency of expression of a specific opioid mu receptor gene SNP A118G

- The segmental duplication data are provided to us through an outside collaborator. This person is currently working on that data and says that it will be available to us in about two

Why are segmental duplications (Low Copy Repeats/LCRs) omitted from the March 2006 UCSC Genome

Hi I'm no longer seeing any options to show tracks for SNPs or segmental duplications. Is this

I am happy to see that you have a new human build out (HG18). I notice you do not yet have the

to the Segmental Dups track that Jen mentioned, you can also see this in the WSSD Duplication and Self Chain tracks. OCLN lies just on the edge of this range. You can see by viewing the Known

Hi, I want to compare 18p and 16q for any homology between them their sequence or segmental

, >segmental duplications) within a defined region of a chromosome. I have >tried a variety of searches using the table brower with intersecting tables >with no success