Dear Colleagues, I am trying to get the orthologous/homologous regions from hg18 multiz28way maf files for a list of human coordinates. I have read the documents and track descriptions, but still have several questions:
1. The results from mafFrags lost the genomic coordinate information for all the query species, and one maf block for each coordinate region in input bed file. It may contain genomic breaks in some species, that is, the corresponding sequence for a query species (say, rheMac2) in the maf block is composed of different genomic locations (from the same or different chromosomes). I derive this based on the net alignment construction procedure. I need to know this information and exclude these cases because they are artificial and not true sequences. How can I get the genomic breaks in the results from mafFrags? When I checked the alignment in the UCSC browser, they are given in different blocks, which seems based on genomic breaks in any species. 2. In the mafFrags results, there are two symbols indicating gaps. One is dash '-', and the other is dot '.'. I think dash is the real gaps in query sequences, but what does the dot represent? Does it represent unsequenced regions or gaps too? 3. In the net alignment construction, the gaps in the top level chain are filled by trimmed lower-scoring chains. What is the minimum length for gaps to be filled? Is 1-base long gap in top level chain also filled by lower-scoring chain? 4. During net alignment process, are the unsequenced regions (N's) regarded as gaps and filled during this process? Thank you in advance! Zhenguo -- —————————————————————— Zhenguo Zhang Postdoctoral Scholar Institute of Molecular Evolutionary Genetics Penn State University 312 Mueller Lab, University Park, PA 16802 Tel: 814-865-2796 Homepage: http://www.personal.psu.edu/zuz17/ Lab: http://homes.bio.psu.edu/people/Faculty/Nei/ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
