Summary of files in http://bio.cse.psu.edu/mousegroup/Evolutionary_Rates/

These files have data and/or results of the analysis of blastz alignments of the human genome with the mouse genome.

• AlnPid_GenPar_SO_PSUCSC.txt data for measures of alignment, interspersed repeat density, GC content and many other genomic parameters for the human genome, 1 Mb nonoverlapping windows
• AlnPid_GenPar_SO_PSUCSC_descrip describes the data in AlnPid_GenPar_SO_PSUCSC.txt
• aln_pid_PSUCSC1-6.pdf graphs of variation in coverage by alignments (aln) and percent identity overall, in neutral sites and in exons for human chromosomes 1- 6.
• aln_pid_PSUCSC7-12.pdf graphs of variation in coverage by alignments (aln) and percent identity overall, in neutral sites and in exons for human chromosomes 7- 12.
• aln_pid_PSUCSC13-18.pdf graphs of variation in coverage by alignments (aln) and percent identity overall, in neutral sites and in exons for human chromosomes 13-18.
• aln_pid_PSUCSC19-X.pdf graphs of variation in coverage by alignments (aln) and percent identity overall, in neutral sites and in exons for human chromosomes 19-X.
• frxn_sel_kernel.pdf frxn_sel_kernel.pdf fraction of alignments under selection, first approach
• kernel_share_smoothing.pdf fraction of alignments under selection; kernel analysis for estimation of the functional share; high smoothing
• kernel_share_smoothing_t.pdf fraction of alignments under selection; kernel analysis for estimation of the functional share; t-modeling results
• pca_figs.pdf multivariate analysis to explain variation in conservation, principal component analysis
• reg_figs.pdf multivariate analysis to explain variation in conservation, regression analysis
• alu_YO_aln_figs2.pdf examination of distribution of Alu repeats (young and old) as a function of conservation of the DNA
• lowGC_noDeltaGC_descr_prop.pdf describes a subset of the human genome that is very low in GC and has changed very little in GC content between mouse and human. These segments tend to be juxtaposed in the genome, and many comprise Giemsa-dark bands with a paucity of known or predicted genes.
• 1mb-win+1mb-slide/ This folder is an un-compressed set of files from UCSC with percent identity data at neutral sites and exons. It is provided for ease of access.
• All_aln2.gz
• rev_all.gz
• all_per_rev.gz
• Aln0717.gz
• ALL_den31_1M.txt
• ALL_den31_51.txt
• ALL_den31_55.txt