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aantakeningen.txt
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# R-code voor alle menselijke motifs
human_jaspar = subset (MotifDb, organism=='Hsapiens' & dataSource=='JASPAR_2014')
matrices = MotifDb [human_jaspar]
print(as.list(matrices))
# 318 motifs
#
# This library was provided courtesy of Boris Lenhard and the JASPAR database (http://jaspar.cgb.ki.se/) on October 15, 2009.
#
# The motifs were parsed from the files available on the JASPAR ftp server:
# [1] http://jaspar.genereg.net/html/DOWNLOAD/all_data/matrix_only/matrix_only.txt
# [2] http://jaspar.genereg.net/html/DOWNLOAD/all_data/FlatFileDir/matrix_list.txt
# A pseudocount was added to each count in the base count matrix prior to conversion to a frequency matrix.
# Note that JASPAR allows multiple species to be assigned to a motif, whereas MochiView does not.
# In the 16 cases where this occurred, the species list is provided in the description and precedence
# was given to Homo sapiens and then Mus musculus (this covered all cases).
#
# 19 species are represented in the JASPAR library (this file only includes entries assigned to Homo sapiens):
# Antirrhinum majus: 3 motif(s)
# Arabidopsis thaliana: 5 motif(s)
# Caenorhabditis elegans: 24 motif(s)
# Drosophila melanogaster: 128 motif(s)
# Gallus gallus: 2 motif(s)
# Halocynthia roretzi: 1 motif(s)
# Homo sapiens: 318 motif(s)
# Hordeum vulgare: 1 motif(s)
# Mus musculus: 428 motif(s)
# Oryctolagus cuniculus: 1 motif(s)
# Petunia hybrida: 1 motif(s)
# Pisum sativum: 3 motif(s)
# Rattus norvegicus: 7 motif(s)
# Rattus rattus: 1 motif(s)
# Saccharomyces cerevisiae: 177 motif(s)
# Triticum aestivum: 1 motif(s)
# Xenopus laevis: 1 motif(s)
# Zea mays: 6 motif(s)
# Unlisted Species: 208 motif(s)
#
# JASPAR: an open-access database for eukaryotic transcription factor binding profiles
# Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D91-4
# Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B.
# JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
# Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A.
# Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6. Epub 2007 Nov 15.
#
# Medline IDs for individual motifs can be found in the description lines of each motif. Full abstracts
# and references for these IDs (matched to motif name) are available on the MochiView website.
#
# Bash-code voor downloaden en uitpakken menselijk genoom
wget -r -nd -X /genomes/H_sapiens/ARCHIVE,/genomes/H_sapiens/ARCHIVE -t 45 --accept="hs_ref_GRCh38.p2_chr*.gbk.gz" "ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens*"
gunzip *.gz