EpiDope: Prediction of B-cell epitopes from amino acid sequences
Features
- Fast genome wide search
- Interactive graphical results
- Docker support
Download
- Download from GitHub
Reference
[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.
Features
- From input fasta to prediction of host in seconds.
Download
- Download from GitHub
Reference
[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.
Download
- Download from GitHub
Reference
[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.
Download
- Download from GitHub
Reference
[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
Download
- 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
Download
- 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
Download
- Go to web server
- Source code @GitHub
- Run PCAGO as standalone desktop application using the Electron framework
Reference
[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.
Download
Reference
[bibtex file=https://raw.githubusercontent.com/rnajena/literature/master/webpage_literature.bib key=Fricke:16]VrAP: Viral Assembly Pipeline
VrAP is no longer maintained.
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
Download
RNAgraphdist: Graph distance between to bases
RNAgraphdist is no longer maintained.
Features & Facts
- Handles thousands of input constraints
- Plots all results with gnuplot
- Optimized for multi-cores
- Runtime complexity: O(n log n)
Download
References
[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.
Features & Facts
- Based on the whole set of all known bacterial orthologous genes and their syntenic information determined by Proteinortho
Download
Proteinortho: Orthology detection tool
Proteinortho is no longer maintained.
Features & Facts
- Small memory footprint
- Optimized for multi-core and cluster environments
- Runtime complexity: O(n2)
Download
Galculator: Nucleotide counter for fasta files
Galculator is no longer maintained.
Features & Facts
- Small constant memory footprint
- Handles hundreds of petabytes if necessary
- Runtime complexity: O(n)