Motif Databasesdoi:10.1007/3-540-29623-9_7882A motif database contains representations of conserved sequences, for annotation of unknown sequences by comparison with individual, known sequences. Protein DatabasesSpringer Berlin Heidelberg
The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for...
必看综述:An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data - Qin Ma DNA motif databases and their uses 目前的金标准数据库: TRANSFAC JASPAR【CORE collection】 HOCOMOCO CIS-BP DBcorrDB【我用的罕见的EZH2和HDAC就是这里下载的】 TFBS鉴定工具: MEME HOMER TFBS...
Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb...
python create_cistarget_motif_databases.py -f Ath.promoter3K.V2.fa -M motif_cb_format/ -m Ath.TF.txt -o Athaliana -t 30 但是报错了。 报错文件 看报错文件,才发现原来create_cistarget_motif_databases.py程序中自己要去运行cbust,不是基于我运行的结果去解读。
Motif databases are used in the function and structure prediction of proteins which appear on new and rapid release of raw data from genome sequencing projects. Recently, the frequency of use about these databases increases continuously. However, existing motif databases were developed and extended ind...
Motif Databases included in HOMER- HOMER最常使用的一些motif数据库 HOMER的motif格式 jaspar- 最全的转录因子数据库 下载所有human的TF对应的motif:链接 下载JASPER上的转录因子及其motif数据库,这部分很重要是因为我们不仅需要motif的信息,而且需要motif对应的人类转录因子的信息。【需要用homer的工具进行格式转换】 ...
The invention relates to sequences of specific mitochondrial proteins that bind, transport and/or regulate intracellular calcium ions. The invention identifies these amino acid sequences and nucleotide sequences encoding them in databases of biological sequences for which subcellular localization and functio...
网页版的meme太慢了,下载了本地版在linux上跑,在用centrimo的时候需要和数据库里的motif比对,所以数据库也需要下载。 在JASPAR中下载meme格式,发现是一个压缩包里几千个分开的motif文件,找半天没看到整个plant的pfm文件,终于在meme网站左边看见Databases下面还有个Download & Install,于是直接下载Motif Databases。
motifRankings <- importRankings("~/databases/hg19-tss-centered-10kb-7species.mc9nr.feather") # Motif enrichment analysis: motifEnrichmentTable_wGenes <- cisTarget(geneLists, motifRankings, motifAnnot=motifAnnotations_hgnc) 数据库实例(子集)