EpiDope: Prediction of B-cell epitopes from amino acid sequences
  • Fast genome wide search
  • Interactive graphical results
  • Docker support
[bibtex file=https://raw.githubusercontent.com/rnajena/literature/master/webpage_literature.bib key=Collatz:20]
VIDHOP: virus host prediction

VIDHOP is a fast and accurate deep learning approach for viral host prediction, which is based on the viral genome sequence only. VIDHOP allows highly accurate predictions while using only fractions (100–400 bp) of the viral genome sequences. VIDHOP also allows the user to train and use models for other viruses.

  • From input fasta to prediction of host in seconds.
[bibtex file=https://raw.githubusercontent.com/rnajena/literature/master/webpage_literature.bib key=Mock:20]
RNAflow: Simple RNA-Seq differential gene expression pipeline using Nextflow
RNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data’s computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies.

RNAflow is a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus.

[bibtex file=https://raw.githubusercontent.com/rnajena/literature/master/webpage_literature.bib key=Lataretu:20]
SIM: SilentMutations
SilentMutations (SIM) can analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. It simulates destructive and compensatory mutants of two key regions from a single-stranded RNA, which can then be utilized for the combinatorial in vitro analysis of RNA-RNA interactions.

[bibtex file=https://raw.githubusercontent.com/rnajena/literature/master/webpage_literature.bib key=Desiro:18]
GORAP: Genomewide ncRNA Annotation Pipeline
GORAP is a pipeline for automated non-coding RNA annotation based on BioPerl, Infernal, Blast, RNAmmer, tRNAscan, Bcheck, RAxML, CRT, Mafft, Samtools.

Features & Facts
  • Input: FASTA file(s)
  • Uses in-house filters (e.g. phylogeny based) and TPM/FPKM computation from BAM files
  • Offers RNome based phylogeny reconstruction
  • Root less installation for Linux, Unix
  • Requirements: internet, gcc, wget, Perl, make
  • Easy–installer including all necessary software, libraries and up to date databases (Rfam, NCBI Taxonomy, Silva)
  • Source @GitHub
PoSeiDon: Positive Selection Detection and Recombination Analysis
PoSeiDon is an easy-to-use pipeline to detect significant positively selected sites and possible recombination events in an alignment of multiple coding sequences.

Features & Facts
  • Input: nucleotide coding sequences as one multiple FASTA file
  • assigns unique ID that can be used to access all data when calculations are finished
  • GitHub page
  • PoSeiDon now runs w/ Nextflow and Docker: nextflow run hoelzer/poseidon --help
PCAGO: Principal component analysis for RNA-Seq read counts
PCAGO is an interactive web service that helps you analyze your RNA-Seq read counts with principal component analysis (PCA) and clustering.

Features & Facts
  • read count normalization
  • download annotations and GO terms for your genes
  • tool to find gene variance cut-off for PCA
[bibtex file=https://raw.githubusercontent.com/rnajena/literature/master/webpage_literature.bib key=Gerst:18]
LRIscan: Long range RNA-RNA interactions
LRIscan is no longer maintained.
LRIscan is a tool to predict conserved, genome-wide long range RNA-RNA interactions based on a multiple sequence alignment in only a few hours on an average computer.

[bibtex file=https://raw.githubusercontent.com/rnajena/literature/master/webpage_literature.bib key=Fricke:16]
VrAP: Viral Assembly Pipeline
VrAP is no longer maintained.
VrAP is a viral assembly pipeline based on the genome assembler SPAdes combined with an additional read correction and several filter steps. VrAP classifies the contigs to distinguish host from viral sequences by annotation and ORF density scores.

Features & Facts
  • new ORF density method to identify viruses without any sequence homology to known references
  • tested on real datasets generated with different sequencing technologies


RNAgraphdist: Graph distance between to bases
RNAgraphdist is no longer maintained.
RNAgraphdist finds the shortest graph distance between to bases i and j.

Features & Facts
  • Handles thousands of input constraints
  • Plots all results with gnuplot
  • Optimized for multi-cores
  • Runtime complexity: O(n log n)
[bibtex file=https://raw.githubusercontent.com/rnajena/literature/master/webpage_literature.bib key=Qin:14,Backofen:13]
POMAGO: Multiple Genome Aligner
POMAGO is no longer maintained.
POMAGO is a multiple genome aligner designed for, but not limited to, bacterial genomes.

Features & Facts
  • Based on the whole set of all known bacterial orthologous genes and their syntenic information determined by Proteinortho
Proteinortho: Orthology detection tool
Proteinortho is no longer maintained.
Proteinortho is a tool to detect orthologous proteins across hundreds of species.

Features & Facts
  • Small memory footprint
  • Optimized for multi-core and cluster environments
  • Runtime complexity: O(n2)
Galculator: Nucleotide counter for fasta files
Galculator is no longer maintained.
Galculator is a nucleotide counter for fasta files that counts mononucleotide frequencies, dinucleotide frequencies, and gapped dinucleotide frequencies (XnY).

Features & Facts
  • Small constant memory footprint
  • Handles hundreds of petabytes if necessary
  • Runtime complexity: O(n)