This directory contains the Build 35 finished human genome assembly (hg17, May 2004). The chromosomal sequences were assembled by the International Human Genome Project sequencing centers. Files included in this directory: chromAgp.zip - Description of how the assembly was generated, unpacking to one file per chromosome. chromFa.zip - The assembly sequence in one file per chromosome. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. Repeat masking was done using the following RepeatMasker/RepBase versions: RepBase Update 8.12, RM database version 20040130. The main assembly is found in the chrN.fa files, where N is the name of the chromosome. The chrN_random.fa files contain clones that are not yet finished or cannot be placed with certainty at a specific place on the chromosome. In some cases, including the human HLA region on chromosome 6, the chrN_random.fa files also contain haplotypes that differ from the main assembly. chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were created by RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period of less than or equal to 12, and translated into one .bed file per chromosome. contigAgp.zip - Description of how the assembly was generated from fragments at a contig layout level. contigFa.zip - The assembly sequence contigs, in one file per NCBI contig. All contigs are in forward orientation relative to the chromosome. In some cases, this means that contigs will be reversed relative to their orientation in the NCBI assembly. Repeats from RepeatMasker and Tandem Repeats Finder are shown in lower case; non-repeating sequence is shown in upper case. contigFaMasked.zip - The assembly sequence contigs, in one file per contig. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. contigOut.zip - RepeatMasker .out file for contigs. These were created by RepeatMasker at the -s sensitive setting. contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, and translated into one .bed file per contig. est.fa.gz - Human ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. liftAll.zip - Offsets of contigs within chromosomes. mrna.fa .gz - Human mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updated once a week via automatic GenBank updates. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts for RefSeq genes with annotated 5' UTRs. This file is updated weekly so it could be slightly out of sync with the RefSeq data which is updated daily for most assemblies. upstream2000.zip - Same as upstream1000, but 2000 bases. upstream5000.zip - Same as upstream1000, but 5000 bases. xenoMrna.fa.gz - GenBank mRNAs from species other than that of the genome. This sequence data is updated once a week via automatic GenBank updates. hg17.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. ----------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend that you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/hg17/chromosomes. To download multiple files, use the "mget" command: mget ... - or - mget -a (to download all the files in the directory) All the files in this directory are freely available for public use.