This directory contains data from the December 2007 ENCODE Multi-Species
Sequence Analysis (MSA) sequence freeze, along with multiple sequence
alignments based on these sequences. The freeze consists of sequence
from regions orthologous to the human ENCODE regions in 36 vertebrate
species, and are based on comparative sequence data generated at the
NHGRI Intramural Sequencing Center (NISC) for the ENCODE project,
as well as whole-genome assemblies residing at UCSC, as listed:
New species in this freeze are:
orangutan
Species from previous freezes not present in this freeze are:
xenopus, fugu, zebrafish, tetraodon
NISC sequences are present in additional regions, and WGS genomes
have all been updated to the most current.
* human (March 2006, hg18)
* armadillo (NISC)
* baboon (NISC)
* cat (NISC)
* chicken (galGal3)
* chimp (Mar 2006, panTro2)
* colobus_monkey (NISC)
* cow (Aug 2006, bosTau3)
* dog (May 2005, canFam2)
* dusky_titi (NISC)
* elephant (NISC)
* flying_fox (NISC)
* galago (NISC)
* gibbon (NISC)
* guinea_pig (NISC)
* hedgehog (NISC)
* horse (NISC)
* macaque (Jan 2006, rheMac2)
* marmoset (NISC)
* monodelphis (Jan 2006, monDom4)
* mouse (Jul 2007, mm9)
* mouse_lemur (NISC)
* orangutan (Jul 2007, ponAbe2)
* owl_monkey (NISC)
* platypus (NISC)
* rabbit (NISC)
* rat (Nov 2004, rn4)
* rfbat (NISC)
* rock_hyrax (NISC)
* sbbat (NISC)
* shrew (NISC)
* squirrel_monkey (NISC)
* st_squirrel (NISC)
* tenrec (NISC)
* tree shrew (NISC)
* vervet (NISC)
DIRECTORY STRUCTURE:
sequences/${ENCODE_REGION}/${COMMON_NAME}.${ENCODE_REGION}.fa
sequences/metadata.txt description of all of the sequences; same as header lines
DEC-2007.tar.gz tarfile of the contents of the sequences directory
encode_36way.gif phylogenetic tree image
species36.nh phylogeny in newick tree format
tree_4d.tba.nh phylogeny with branch lengths, based on 4-fold degenerate sites
alignments/ multiple sequence alignments
Each FASTA file will have all the sequence entries for a given
species/region.
Description of the FASTA Header lines and the metadata.txt file:
>${COMMON_NAME}|${ENCODE_REGION}|${FREEZE_DATE}|${NCBI_TAXON_ID}|${ASSEMBLY_PROVIDER}|${ASSEMBLY_DATE}|${ASSEMBLY_ID}|${CHROMOSOME}|${CHROMOSOME_START}|${CHROMOSOME_END}|${CHROMOSOME_LENGTH}|${STRAND}|${ACCESSION}.${VERSION}|${NUM_BASES}|${NUM_N}|${THIS_CONTIG_NUM}|${TOTAL_NUM_CONTIGS}|${COMMENT}
Where:
${COMMON_NAME} like 'baboon' or 'dusky_titi'
${ENCODE_REGION} like 'ENm001' or 'ENr223'
${FREEZE_DATE} like 'AUG-2004'; latest date for inclusion in this freeze of the set of sequences encompassing the ENCODE regions
${NCBI_TAXON_ID} like '9555' or '9523'
${ASSEMBLY_PROVIDER} like 'NISC' or 'RGSC'
${ASSEMBLY_DATE} like 'NOV-2003' or '21-JUN-2003'; Date associated with the specific sequence assembly represented in this ENCODE freeze
${ASSEMBLY_ID} like 'rn4' or 'panTro2'
${CHROMOSOME} like 'chr1' or 'chr19_random'
${CHROMOSOME_START} [1 based]
${CHROMOSOME_END} [1 based]
${CHROMOSOME_LENGTH} length of entire ${CHROMOSOME}
${STRAND} as in '+' or '-' indicating whether the sequence came from the top or bottom DNA strand
${ACCESSION}.${VERSION} like 'NT_107546.1' or internal identifier for assemblies that have not been accessioned yet.
${NUM_BASES} Total number of called bases in the sequence entry, including N's
${NUM_N} Total number of N's in the sequence entry
${THIS_CONTIG_NUM} ID of sequence contig (see next variable).
${TOTAL_NUM_CONTIGS} Total number of sequence contigs syntenic to a human region.
${COMMENT} This is an example I hope we all agree on. (Currently '.' for all entries.)
>rat|ENm001|May-2005|10116|Baylor HGSC v. 3.1|01-Jun-2003|rn3|chr4|42742602|44711183|187371129|+|NT_107460.3|1968582|143786|1|1|.
Some fields are optional. For example when ${ASSEMBLY_PROVIDER} ==
NISC, there will be no ${ASSEMBLY_ID} or chrom:start-stop coordinates.
Unused fields are filled with a period ('.') or zero ('0') for ease in
parsing.
The FASTA sequence have been repeat masked with default RepeatMasker
options and with the Tandem Repeat Finder. Repeat sequences are
indicated in lowercase, while non-repeat sequences are in uppercase.
These are the RepeatMasker library options that were used here:
armadillo => mammal
baboon => mammal
cat => cat
chicken => chicken
chimp => mammal
colobus_monkey => mammal
cow => cow
dog => dog
dusky_titi => cow
elephant => mammal
flying_fox => mammal
galago => mammal
gibbon => mammal
guinea_pig => mammal
hedgehog => mammal
horse => mammal
human => human
macaque => mammal
marmoset => mammal
monodelphis => mammal
mouse => mus
mouse_lemur => mammal
orangutan => mammal
owl_monkey => mammal
platypus => mammal
rabbit => rodentia
rat => rat
rfbat => mammal
rock_hyrax => mammal
sbbat => mammal
shrew => mammal
squirrel_monkey
st_squirrel => mammal
tenrec => mammal
tree_shrew => mammal
vervet => mammal
There are also a set of RECON libraries that have been prepared by
Damian Keefe at EBI.
ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/repeat_libraries/
Data Release Terms
------------------
All data in this directory and any subdirectories are subject to the terms
of the ENCODE Project Data Release Policy of the National Human Genome Research
Institute. This policy is posted at:
http://www.genome.gov/12513440
http://genome.ucsc.edu/encode/terms.html
Name Last modified Size Description
Parent Directory -
DEC-2007.tar.gz 2008-02-20 09:51 296M
sequences/ 2008-06-25 10:05 -
tree_4d.tba.nh 2008-08-21 10:53 1.0K
alignments/ 2008-08-21 12:14 -
species36.nh 2008-10-22 16:23 376
encode_36way.gif 2008-10-22 16:33 6.4K