The kent program hgGcPercent will measure what you want to measure from your sequences.
--Hiram hgGcPercent - Calculate GC Percentage in 20kb windows usage: hgGcPercent [options] database nibDir nibDir can be a .2bit file, a directory that contains a database.2bit file, or a directory that contains *.nib files. Loads gcPercent table with counts from sequence. options: -win=<size> - change windows size (default 20000) -noLoad - do not load mysql table - create bed file -file=<filename> - output to <filename> (stdout OK) (implies -noLoad) -chr=<chrN> - process only chrN from the nibDir -noRandom - ignore randome chromosomes from the nibDir -noDots - do not display ... progress during processing -doGaps - process gaps correctly (default: gaps are not counted as GC) -wigOut - output wiggle ascii data ready to pipe to wigEncode -overlap=N - overlap windows by N bases (default 0) -verbose=N - display details to stderr during processing -bedRegionIn=input.bed Read in a bed file for GC content in specific regions and write to bedRegionsOut -bedRegionOut=output.bed Write a bed file of GC content in specific regions from bedRegionIn example: calculate GC percent in 5 base windows using a 2bit assembly (dp2): hgGcPercent -wigOut -doGaps -win=5 -file=stdout -verbose=0 \ dp2 /cluster/data/dp2 \ | wigEncode stdin gc5Base.wig gc5Base.wib ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/