Pipelines

This page contains a list of all pipelines that you can access from W2H. Click on the name of the pipeline to get a more detailed description and some example output. Pipelines are organized in groups:

NGS Analysis

OnTarget OnTarget evaluates data from next-generation sequencing after subgenomic enrichment. It processes sequence reads and maps them against target regions of the genome.
PeakDetector ChipSeq Peak Detection.
NextGene NextGene extracts genes close to or overlapping with given genomic regions.
FilterReads FilterReads trims and cleans sequence reads.
SplicingCompass SplicingCompass finds differentially spliced genes.
TargetCoverage TargetCoverage computes the coverage of target regions (e.g. complete set of exons) with sequence reads.
ChiPeAn ChiPeAn is a pipeline to analyse Chipseq data. It searches for known transcription factor binding sites, analyses the neighborhood of the peaks and performs GO and KEGG enrichment, motif comparison and motif enrichment analysis.
srnaMapper Quality control, filtering, and (optional) mapping pipeline mainly for small RNA data
ncRNAAnnotator Classification (Annotation) of non-coding RNAs
CompaRNA Comparison of two ncRNA experiments
ncRNAPredictor Prediction of new non-coding RNAs
Contaminator Detect contaminating sequences in high throughput data
evalRSeq Assessment of RNA-Seq Quality
FastRNAMapper Count and Coverage Analysis of RNA-Seq data
GeneCoverage Coverage Analysis of Selected Genes in Sequencing Experiments
GenePanelCoverage Theoretical read coverage of genes when using enrichment kits
Ontarget2 Ontarget2 evaluates NGS data coverage after subgenomic enrichment
Methan Methylation Analysis of bisulfite treated sequences
PeptideDisplayAnalysis Filters the input reads from Phage display and lists the inserts according to their frequency
PepEnrich Enrichment Analysis of several Rounds of PeptideDisplayAnalysis

Protein Analysis

2dSweep 2DSweep is a task analysing various secondary structure elements of proteins. It employs multiple algorithms for predicting features like alpha-helices, beta-strands, transmembrane regions, signal sequences, and many other as well.
DomainSweep DomainSweep identifies the domain architecture within a protein sequence and thus can help to find correct functional assignments for an uncharacterised protein sequence. It employs different database search methods to scan a number of protein domain/family databases. The result comprises an overview of the different database search results and a graphical report about the location of family patterns.
GOPet GOPET ( Gene Ontology term Prediction and Evaluation Tool) is an automatic sequence annotation tool. The program predicts molecular function or biological process Gene Ontology (GO) terms of nucleotide and protein sequences with defined confidence values. The prediction is achieved by using specific GO-annotated sequence databases in combination with multiple Support Vector Machines. Multiple predictions are combined by applying a committee approach.
GOPet2D GOPET2D is a variant of GoPet to predict molecular function GO terms for unknown protein sequences by using predicted secondary structure features of the protein in combination with Support Vector machines.
ProtSweep Protsweep is a protein annotation pipeline, based on homology searches. It uses a cascading database search strategy to find the best hit possible and then extracts annotation information from different databases.

MiRNA Analysis

miRpredict miRpredict is a tool for analyzing a potential miRNA by comparing it to known miRNAs, by localizing it on the genome, and by analyzing the 2D structure of its potential precursor.
miRTaCa miRTaCa is a tool for predicting binding sites for miRNA in 3'-untranslated regions of mRNAs.
TargetscanPLUS TargetscanPlus is a pipeline for identifying microRNA target sites in UTR sequences. It is based on TargetScan and improves the results by applying an SVM-classifier based on alternative models.

gene/exon/splicing/promoter

AASsites AASsites is a pipeline to predict gene structure changes due to Single Nucleotide Polymorphisms (SNPs) or other mutations.
CrypSkip Crypskip is a program to analyse whether a mutated sequence favours cryptic splice site activation or exon skipping.
ESEDetector EseDetector is a program for predicting exonic splicing enhancers in human exons. It combines the program EseFinder with a classification schema via Support Vector Machines.
GeneConsensus GeneConsensus is a gene identification program which runs multiple gene prediction programs (like GenScan, HMMGene, and GeneID) and computes a consensus prediction using different algorithms.
SERPredict SERpredict is a tool for analyzing a transcript of a gene which contains a transposable element. It determines if the inclusion of the transposable element created a tissue or tumor-specific isoform.
PromoterSweep PromoterSweep is a pipeline for identifying transcription factor binding sites. It uses a combination of promoter database search tools, binding site identification programs and de novo motif discovery tools to analyse an unknown promoter region.

est/cdna/orf Analysis

Caftan Caftan is a tool for quick mapping, annotation, and quality assessment of cDNAs.
cDNA2Genome cDNA2Genome is an annotation tool that maps a cDNA to genomic data. It combines various kinds of gene prediction programs, database searches and sequence comparison methods.
CloneAnnotation annotation and quality assessment of clones
ESTAnnotator ESTAnnotator tries to identify EST sequences by running BlastN2 searches with different databases and/or extending the EST by clustering with other available homologous EST sequences.

Others

DNASweep DNASweep tries to identify a piece of eukaryotic DNA by homology search and tries to locate possible genes and promoter elements in the sequence.
GenomeBlaster GenomeBlaster compares your input sequence to an entire genome using the MegaBlast algorithm and then provides information about possible features (genes, repeats, etc) of the mapped genomic region.
IntegrationMap No description.
IntegrationSeq No description.
Map2Genome Map2Genome maps DNA sequence(s) to a genome.
MSFGenerator MSFGenerator searches for related sequences to a given protein using a BlastP2 database search. According to user defined rules some of these sequences are selected to create a multiple sequence alignment (MSF-File).
OrfMap OrfMap is a task for displaying restriction sites together with open reading frames graphically.
PATH PATH (Phylogenetic Analysis Task in Husar) is a task that estimates and realizes phylogenies by executing the three main phylogenetic methods: distance, parsimony and maximum likelihood.
PrimerSweep PrimerSweep finds primers or checks pairs for PCR reactions, matching your input sequence and target region. It searches for possible other products using blast with an organism specific database.
UTRPrimer Find primers to amplify the UTR regions of genes for cloning with certain restriction enzymes.
last update:
19/07/2017
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