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 <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All the files in this directory are freely available for public use.
Name Last modified Size Description
Parent Directory -
est.fa.gz.md5 2019-10-17 09:54 44
mrna.fa.gz.md5 2019-10-17 09:34 45
refMrna.fa.gz.md5 2019-10-17 09:55 48
xenoMrna.fa.gz.md5 2019-10-17 09:45 49
xenoRefMrna.fa.gz.md5 2019-10-17 09:55 52
upstream1000.fa.gz.md5 2019-10-17 09:56 53
upstream2000.fa.gz.md5 2019-10-17 09:57 53
upstream5000.fa.gz.md5 2019-10-17 09:58 53
hg17.chrom.sizes 2007-03-02 15:21 792
liftAll.zip 2004-07-23 13:50 5.5K
chromAgp.zip 2004-07-23 11:26 533K
contigAgp.zip 2004-07-23 12:38 592K
chromTrf.zip 2004-07-23 13:50 6.7M
contigTrf.zip 2004-07-23 13:50 7.0M
upstream1000.fa.gz 2019-10-17 09:56 9.3M
upstream2000.fa.gz 2019-10-17 09:57 17M
upstream5000.fa.gz 2019-10-17 09:58 45M
refMrna.fa.gz 2019-10-17 09:55 80M
contigOut.zip 2004-07-23 12:42 150M
chromOut.zip 2004-07-23 11:29 151M
xenoRefMrna.fa.gz 2019-10-17 09:55 250M
mrna.fa.gz 2019-10-17 09:34 370M
contigFaMasked.zip 2004-07-23 16:09 487M
chromFaMasked.zip 2004-07-23 12:38 488M
hg17.2bit 2006-05-15 14:41 767M
contigFa.zip 2004-07-23 13:25 894M
hg17.fa.gz 2020-10-19 13:10 895M
chromFa.zip 2004-07-23 12:13 895M
est.fa.gz 2019-10-17 09:54 1.5G
xenoMrna.fa.gz 2019-10-17 09:45 6.4G