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. 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
