MDC-Berlin: Ohler Lab
Recent and ongoing projects address transcription control (initiation, modeling of enhancers and their evolution, regulatory site identification, decoding enhancers based on sequence and chromatin), small RNAs (identification of microRNAs and targets), expression (condition-specific microarray/sequencing data, spatial expression from microscopy), or the modeling of regulatory networks containing transcription factors and miRNAs.
Tools for download:
Prediction of coding and non-coding genes RSVP
- prediction of alternative isoforms of protein-coding genes, based on both genomic DNA evidence and aligned RNA-seq reads
PIPmiR
- identify novel plant miRNA genes from a combination of deep sequencing data and genomic features
NASTIseq
- identification of cis-Natural Antisense Transcripts (cis-NAT) using strand specific RNA-seq data Promoter and enhancer analysis
S-Peaker
- identify probable locations for single-peak TSSs in an input sequence Orthologous enhancers
- searches for orthologous enhancer region in a related species for a given known enhancer miRNA target prediction
MUMMIE
- MUltivariate Markov Modeling Inference Engine
microMUMMIE
- microRNA target-site prediction in PAR-CLIP data
TargetThermo
- compute predicted expression fold change of a gene caused by a miRNA
WaRSwap
- network motif discovery in large multi-layer networks that include Transcription Factors (TFs), microRNAs (miRNAs), and non-TF protein coding genes.
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