Hello, The utility mafFilter is the best choice: use option -speciesFilter. You do not need to set up the entire code tree or a mirror to use the utilities in the kent source tree.
http://genomewiki.ucsc.edu/index.php/The_source_tree http://hgdownload.cse.ucsc.edu/downloads.html -> Source mafFilter - Filter out maf files. Output goes to standard out usage: mafFilter file(s).maf options: -tolerate - Just ignore bad input rather than aborting. -minCol=N - Filter out blocks with fewer than N columns (default 1) -minRow=N - Filter out blocks with fewer than N rows (default 2) -factor - Filter out scores below -minFactor * (ncol**2) * nrow -minFactor=N - Factor to use with -minFactor (default 5) -minScore=N - Minimum allowed score (alternative to -minFactor) -reject=filename - Save rejected blocks in filename -needComp=species - all alignments must have species as one of the component -overlap - Reject overlapping blocks in reference (assumes ordered blocks) -componentFilter=filename - Filter out blocks without a component listed in filename *-speciesFilter=filename* - Filter out blocks without a species listed in filename Hopefully this helps, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/22/10 1:42 AM, 董珊 wrote: > Dear Genome list, > > I want to ask a question about creat a multiple alignment from pair-wise > alignments from UCSC Genome Blowser. > The whole genome multiple alignment I need is from 12 Drosophila species, > but the multiple alignment data on UCSC Genome Blowser contain 3 excess > species (A. gambiae, A. mellifera and T. castaneum). > > I know there is a complex method to use multiz/TBA to get multiple alignment > from pair-wise alignments. > However, these pair-wise alignments must in MAF format. > But it seems difficult to get the format convert tool on Kent source. > Do you know other method to remove the 3 excess species from the multiple > alignment from UCSC Genome Blowser? > > Thank you very much in advance! > > Best regards! > Shan > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
