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

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.

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