Abhi, The alignment manipulation tools in Galaxy are based on command line programs available as part of bx-python: http://bx-python.trac.bx.psu.edu If you are going to be repeatedly extracting various features from a set of alignments, your best bet is to index them first. To index a maf file: maf_build_index.py -s hg18 chrX.maf (passing the -s option just produces indexes for a particular species, saving time and disk space, if you omit this option your indexes will allow extracting relative to coordinates on all 6 species). This will build an index in "chrX.maf.index" Then to extract: cat my_regions.bed | maf_extract_ranges_indexed.py -p hg18. chrX.maf In this case I assume your bed file's first column contains values like "chrX". The -p option adds a prefix to these, creating "hg18.chrX" to match the appropriate src in the maf file. You can pass any number of maf files to maf_extract_ranges_indexed.py, so if your bed file has regions across the whole genome, you could do something like: cat my_regions.bed | maf_extract_ranges_indexed.py -p hg18. / directory/of/genome/wide/mafs/*.maf See the help for more information: james@uninvisible% maf_extract_ranges_indexed.py - h ~ /projects/bx-python/code/bx-python-trunk Usage: maf_extract_ranges_indexed.py maf_fname1 maf_fname2 ... [options] < interval_file Options: -h, --help show this help message and exit -m MINCOLS, --mincols=MINCOLS Minimum length (columns) required for alignment to be output -c, --chop Should blocks be chopped to only portion overlapping (no by default) -s SRC, --src=SRC Use this src for all intervals -p PREFIX, --prefix=PREFIX Prepend this to each src before lookup -d DIR, --dir=DIR Write each interval as a separate file in this directory -S, --strand Strand is included as an additional column, and the blocks are reverse complemented (if necessary) so that they are always on that strand w/r/t the src species. -C, --usecache Use a cache that keeps blocks of the MAF files in memory (requires ~20MB per MAF) Let me know if you have other questions. -- jt On Jan 23, 2009, at 8:28 AM, Abhi Ratnakumar wrote: