Thanks Brooke, Best, Assaf
On Wed, Aug 31, 2011 at 5:13 AM, Brooke Rhead <[email protected]> wrote: > Hello Assaf, > > One of our engineers has this comment for you: > > "Many of the other significant hits will be in the chain tables. If there > is more than one chain for the same region in the reference sequence, > chances are it is a duplication in the other species. Similarly, to find > duplications in the reference, the self-chain can be used, or the chains to > the reference sequence in the other assembly can be used." > > Note that the Self Chain table is in the "Variation and Repeats" track > group, not with the other chains in the "Comparative Genomics" track group. > You may also be interested in the pairwise alignment data available for > download from > http://hgdownload.cse.ucsc.**edu/downloads.html<http://hgdownload.cse.ucsc.edu/downloads.html>. > Click on the species you are using for reference, then look for the links > under "Pairwise Alignments." > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > > On 08/28/11 07:12, asas asasa wrote: > >> Hi all, >> >> About the multiz genomic alignments (I use those downloaded from the table >> browser in maf format): >> >> I understand each aligned sequence represent the "best" hit to the >> reference >> genomic segment.Is there a way to compare the best hit to other less >> significant hits, in order to know whether the best hit is significantly >> better than other hits ? >> More generally, my problem is to find a simple way to exclude from my >> analyses alignments where it is not clear if the aligned sequences are >> real >> orthologs. >> >> Best, >> Assaf >> ______________________________**_________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
