Free Tools and Software for Genomics, Transcriptomics, CRISPR & Co.
Julian PampelIn the past decade huge advances have been made in the field of biotechnology. With the help of computers experiments run faster – and produce a lot more data. Biology and informatics merge into bioinformatics, but current software and database resources are extremely fragmented.
This is why we compiled on genomics-online.com a list of software and tools which supports you processing and interpreting your experimental data, be that next-generation sequencing, microarray or mass spectrometry.
Table of Contents:
Tools for CRISPR/ Cas9
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| Off-Spotter | Genomics | yes | Off spotter helps in the design of optimal "guide" RNAs (gRNAs) by providing several protospacer adjacent motif (PAM) choices, a run-time definition of the seed and of the allowed number of mismatches. | Link | |
| CrispRVariants | Genomics | yes | CrispRVariants resolves and localizes individual mutant alleles with respect to the endonuclease cut site. Individual variant alleles from either traditional Sanger sequencing or high-throughput CRISPR-Cas9 mutagenesis sequencing experiments can be quantified and visualized. CrispRVariants allows users to detect problems and filter sequences appropriately before estimating mutation efficiency. This toolkit can be easily used to create a variant allele summary plot and accompanying table of counts. CrispRVariants enables immediate comparison of variant spectra between target locations. | Link | |
| CRISPOR | Genomics | yes | CRISPOR assists with guide selection in 120 genomes, including plants and many emerging model organisms, and pre-calculated results for all human coding exons as a UCSC Genome Browser track. Enhanced off-target prediction accuracy. | Link | |
| Breaking CAS | Genomics | yes | Breaking CAS is a versatile system for detecting putative sgRNA off-targets in CRISPR/Cas applications. BreakingCas allows working with all eukaryotic genomes available in the ENSEMBL database, for a detailed inspection of the genomic neighbourhood of every single potential off-target so as to qualitatively assess them. This web server allows specifying the characteristics and parameters of the nuclease to be used, although predefined set are available for several popular Cas proteins. | Link | |
| CRISPR-AnalyzeR for pooled screens caRpools | High-throughput Sequencing | yes | CaRpools is an R package for exploratory data analysis providing CRISPR/Cas9 screen analysis. CaRpools integrates screening documentation and generation of standardized analysis reports. Its open virtual appliance allows analysis without prior programming knowledge and is therefore suited for novice and expert users. | Link | |
| Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout MAGeCK | High-throughput Sequencing | yes | MAGeCK identifies positively and negatively selected sgRNAs and genes in genome-scale CRISPR/Cas9 knockout experiments. The workflow can be partitioned into four steps: read count normalization, mean-variance modeling, sgRNA ranking and gene ranking. MAGeCK outperforms existing computational methods in its control of the false discovery rate (FDR) and its high sensitivity. | Link | |
| ScreenBEAM | High-throughput Sequencing | yes | Screening Bayesian Evaluation and Analysis Method (ScreenBEAM) is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data. | Link | |
| HiTSelect | High-throughput Sequencing | yes | A comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration. | Link | |
| CRISPRs | High-throughput Sequencing | yes | CRISPRs enables the detection of CRISPRs in locally-produced data and consultation of CRISPRs present in the database. If CRISPR-associated (cas) genes are annotated the program will show them as well. | Link |
Tools for Flow Cytometry
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| FlowUtils | Flow Cytometry | yes | FlowUtils provides a package with utilities for flow cytometry data. | Link | |
| FlowQB | Flow Cytometry | yes | FlowQB is a fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads. | Link | |
| fluorescence-minus-one controls | Flow Cytometry | yes | Based on comparison to fluorescence-minus-one the semi-automated algorithm helps in population discovery. Thus transferring the problem into that of one-class classification, as opposed to being an unsupervised learning problem. | Link | |
| immunoClust | Flow Cytometry | yes | ImmunoClust is an automated analysis pipeline for uncompensated fluorescence and mass cytometry data, which consists of two parts. First, cell events of each sample are grouped into individual clusters. Subsequently, a classification algorithm assorts these cell event clusters into populations comparable between different samples. The clustering of cell events is designed for datasets with large event counts in high dimensions as a global unsupervised method, sensitive to identify rare cell types even when next to large populations. | Link | |
| ViSNE | Flow Cytometry | yes | ViSNE allows one to map high-dimensional cytometry data onto two dimensions, yet conserve the high-dimensional structure of the data. | Link | |
| Fluorescence Spectra Analyzer | Flow Cytometry | yes | BioLegend's Fluorescence Spectra Analyzer is useful for the analysis of excitation and emission spectra of commonly used fluorochromes for flow cytometry. | Link | |
| FlowJo | Flow Cytometry | yes | FlowJo is an analysis platform for single-cell flow and mass cytometry analysis. FlowJo provides an intuitive interface, specialized analysis platforms, and open-ended plugin architecture. FlowJo supports your statistical work e.g in immunophenotyping, cell cycle, proliferation, kinetics studies, quantitative population comparison, or plate screening assays. | Link | |
| FCS Express 6 | Flow Cytometry | yes | FCS Express 6 Flow Cytometry and Image Cytometry Software can turn your flow cytometry, image cytometry, and FACS data analysis into results. FCS Express supports you with plots, gates, cell cycle analysis and proliferation analysis. The data can be easily exported to microsoft office. | Link |
Tools for Gel Electrophoresis
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| GelClust | Gel Electrophoresis | GelClust processes gel electrophoresis images and generates the corresponding phylogenetic trees. Unlike the most of commercial and non-commercial related software tools, GelClust is very user-friendly and guides the user from image toward dendrogram through seven simple steps. | Link | ||
| Lablmage 1D | Gel Electrophoresis | yes | A flexible solution with strong image analysis algorithms is provided by Lablmage 1D. The program works for DNA or protein analysis as well as western blotting techniques. Due to its workflow-based concept, this application has become a prime example of software usability | Link | |
| Melanie | Gel Electrophoresis | yes | Melanie provides a flexible interface to visualize, explore and analyze 2D electrophoresis gel images, in order to identify protein markers of interest through differential expression analysis. | Link |
Tools for Gene Expression Microarray
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| R.S. WebTool | Gene Expression Microarry | yes | R.S. WebTool is a user-friendly platform for Monte Carlo-based significance evaluation of pairwise distances. | Link |
Tools for Gene Suppression
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| siRNA at Whitehead | Gene Suppression | yes | This site helps you select siRNAs to knock down your gene of interest. Enter your sequence, choose a pattern for your oligo nucleotides, and Whitehead will present you with a list of oligos matching your criteria. From this list, select those oligos you would like to consider further. All the selected oligos will be BLASTed against RefSeq, UniGene, or Ensembl database. In the BLAST result page, siRNAs can be further filtered to reduce the non-specific target effects. | Link | |
| Lentivectors Toolbox | Gene Suppression | yes | The Lentivcetors Toolbox gives you information about Lentivectors and protocols for production and titration (ELISA / FACS). | Link | |
| Gene Link shRNA design | Gene Suppression | yes | Gene Link shRNA design is a flexible design tool for siRNA and shRNA with custom loop sequence and cloning sites. | Link | |
| Scramble siRNA | Gene Suppression | yes | Scramble siRNA generates a negative control for siRNA. It accepts a short DNA sequence, and returns a scrambled sequence. | Link | |
| ShRNA Tools for RNAi | Gene Suppression | yes | ShRNA Tools for RNAi assists in the selection of empty vectors for cloning in shRNAs. | Link |
Tools for Genomics
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| LOVD 3.0 | Genomics | yes | Free tool for Gene-centered collection and display of DNA variations. | Link | |
| SpliceCenter | Genomics | yes | The tools on SpliceCenter help evaluating the impact of gene splicing variation on specific molecular biology techniques. | Link | |
| GIGA | Genomics | yes | GIGA is an efficient tree building program. It supports phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale. | Link | |
| Phred | Genomics | yes | Phred is a base-calling program for DNA sequence traces. Phred it analyzes the peaks of DNA sequence chromatogram files to call bases, assigning quality scores ("Phred scores") to each base call. | Link | |
| CodonCode Aligner | Genomics | yes | CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection. | Link | |
| DIALIGN | Genomics | DIALIGN aligns multiple sequence with optional user-defined constraints. | Link | ||
| Off-Spotter | Genomics | yes | Off spotter helps in the design of optimal "guide" RNAs (gRNAs) by providing several protospacer adjacent motif (PAM) choices, a run-time definition of the seed and of the allowed number of mismatches. | Link | |
| CrispRVariants | Genomics | yes | CrispRVariants resolves and localizes individual mutant alleles with respect to the endonuclease cut site. Individual variant alleles from either traditional Sanger sequencing or high-throughput CRISPR-Cas9 mutagenesis sequencing experiments can be quantified and visualized. CrispRVariants allows users to detect problems and filter sequences appropriately before estimating mutation efficiency. This toolkit can be easily used to create a variant allele summary plot and accompanying table of counts. CrispRVariants enables immediate comparison of variant spectra between target locations. | Link | |
| CRISPOR | Genomics | yes | CRISPOR assists with guide selection in 120 genomes, including plants and many emerging model organisms, and pre-calculated results for all human coding exons as a UCSC Genome Browser track. Enhanced off-target prediction accuracy. | Link | |
| Breaking CAS | Genomics | yes | Breaking CAS is a versatile system for detecting putative sgRNA off-targets in CRISPR/Cas applications. BreakingCas allows working with all eukaryotic genomes available in the ENSEMBL database, for a detailed inspection of the genomic neighbourhood of every single potential off-target so as to qualitatively assess them. This web server allows specifying the characteristics and parameters of the nuclease to be used, although predefined set are available for several popular Cas proteins. | Link | |
| BioGPS | Genomics | yes | BioGPS serves as a customizable gene annotation portal, with information about gene and protein function | Link | |
| Genome Browser | Genomics | yes | With the Genome Browser you are able to interactively visualize genomic data. Choose between a variety of spezies and search for a specifc section to get detailled information | Link |
Tools for High-throughput Sequencing
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| SAMtools | High-throughput Sequencing | yes | SAMtools is a suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. Another feature is to index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. | Link | |
| CRISPR-AnalyzeR for pooled screens caRpools | High-throughput Sequencing | yes | CaRpools is an R package for exploratory data analysis providing CRISPR/Cas9 screen analysis. CaRpools integrates screening documentation and generation of standardized analysis reports. Its open virtual appliance allows analysis without prior programming knowledge and is therefore suited for novice and expert users. | Link | |
| Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout MAGeCK | High-throughput Sequencing | yes | MAGeCK identifies positively and negatively selected sgRNAs and genes in genome-scale CRISPR/Cas9 knockout experiments. The workflow can be partitioned into four steps: read count normalization, mean-variance modeling, sgRNA ranking and gene ranking. MAGeCK outperforms existing computational methods in its control of the false discovery rate (FDR) and its high sensitivity. | Link | |
| ScreenBEAM | High-throughput Sequencing | yes | Screening Bayesian Evaluation and Analysis Method (ScreenBEAM) is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data. | Link | |
| HiTSelect | High-throughput Sequencing | yes | A comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration. | Link | |
| CRISPRs | High-throughput Sequencing | yes | CRISPRs enables the detection of CRISPRs in locally-produced data and consultation of CRISPRs present in the database. If CRISPR-associated (cas) genes are annotated the program will show them as well. | Link | |
| EBARDenovo | High-throughput Sequencing | yes | EBARDenovo is a highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. | Link | |
| Blast2GO | High-throughput Sequencing | yes | Blast2GO is spepcialized for annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. With the help of an algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations Blast2GO optimizes function transfer from homologous sequences. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. | Link | |
| CodingQuarry | High-throughput Sequencing | yes | CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts. Predictions are made directly from transcript sequences which is possible through the high quality of fungal transcript assemblies. Correct predictions are made despite transcript assembly problems, including those caused by overlap between the transcripts of adjacent gene loci. | Link | |
| HOMER | High-throughput Sequencing | yes | HOMER consists out of suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. | Link | |
| NGS-QC | High-throughput Sequencing | yes | NGS-QC (Next Generation Sequencing Quality Control Generator) is a computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. | Link | |
| kmerHMM | High-throughput Sequencing | yes | KmerHMM is suited for Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov Model and Belief Propagation. | Link | |
| CexoR | High-throughput Sequencing | yes | CexoR enables strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package 'idr'. | Link | |
| HATSEQ | High-throughput Sequencing | yes | HATSEQ identifies functional regions of interest (ROIs) on the genome where a genomic signal significantly deviates from the general genome-wide behavior. The program provides different visualizations and statistical summaries for the detected ROIs and includes a number of built-in post-analyses with which biological meaning can be attached to the detected ROIs in terms of gene pathways and de-novo motif analysis. No further knowledge of scripting languages required. | Link | |
| plasmidSPAdes | High-throughput Sequencing | yes | PlasmidSPAdes assembles plasmids from whole genome sequencing data. It utilizes SPAdes for transforming the de Bruijn graph into the assembly graph and finds a subgraph of the assembly graph that we refer to as the plasmid graph. It further uses ExSPAnder for repeat resolution in the plasmid graph using paired reads and generates plasmidic contigs. | Link | |
| PlasmidFinder 1.3 | High-throughput Sequencing | yes | PlasmidFinder 1.3 identifies plasmids in total or partial sequenced isolates of bacteria. PlasmidFinder can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The current database consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. The program detects a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens. | Link | |
| OrfM | High-throughput Sequencing | yes | OrfM rapidly identifies open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Ist up to five times faster than comparable tools like ‘GetOrf’ and ‘Translate’. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers. | Link | |
| IGV | High-throughput Sequencing | yes | The Integrative Genomics Viewer (IGV) can be used to explore large integrated genomic datasets and visualize them. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. | Link | |
| FastQC | High-throughput Sequencing | yes | A quality control tool for high throughput sequence data. | Link | |
| Picard | High-throughput Sequencing | yes | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. | Link | |
| CLC Workbench | High-throughput Sequencing | yes | The CLC Workbench combines many useful features for DNA, RNA, and protein sequence data analysis. The features include: Editor for graphically and algorithmically advanced primer design/ Assembly of DNA sequence data/ Molecular cloning /Advanced RNA structure prediction and editing/ Integrated and advanced gene expression analysis /Integrated 3D molecule view | Link |
Imaging Software
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| Fluorescence SpectraViewer | Mass Spectronomy | yes | Fluorescence SpectraViewer allows you to compare multiple dyes in excitation and emission lentgh. Additionally design and select a combination of cell structure probes. | Link | |
| ImageJ | Mass Spectronomy | yes | ImageJ is a powerful tool to analyse and process images in Java. Supports smoothing, sharpening, edge detection, median filtering and thresholding on both 8-bit grayscale and RGB color images. Measure area, mean, standard deviation, min and max of selection or entire image. Measure lengths and angles. Use real world measurement units such as millimeters. Generate histograms and profile plots. | Link | |
| SnapGene | Mass Spectronomy | yes | SnapGene assists you in planning and simulating DNA manipulations, visualizing ORFs, reading frames, and primer binding sites. It also automatically records the steps in a cloning project. | Link | |
| SnapGene Viewer | Mass Spectronomy | yes | SnapGene Viewer is designed to create, browse, and share richly annotated DNA sequence files up to 1 Gb in length. Enter your own sequence, or import a record from GenBank. Browse or print a DNA sequence and its annotations using customizable Map, Sequence, Enzymes, Features, Primers, and History views. Search a DNA sequence to match either a DNA query, or a protein translation, or an annotation. Design and annotate primers for PCR, sequencing, or mutagenesis. Identify open reading frames (ORFs) with a single mouse click. | Link | |
| Pymol | Mass Spectronomy | yes | Pymol is a molecular visualization system. Pymol is able to view and present 3D molecular structures, and render and animate molecules dynamically. | Link |
Mass Spectronomy Tools
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| BioNumerics | Mass Spectronomy | yes | A fully featured application for complete analysis and databasing of two-dimensional gels can be found in BioNumerics. | Link | |
| gel2de | Mass Spectronomy | yes | Gel2DE is able to perform pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. | Link | |
| Novor | Mass Spectronomy | yes | Novor is a real-time peptide de novo sequencing engine that achieved an order-of-magnitude improvement on speed while maintaining the accuracy. It is free of charge for academic research purposes. | Link | |
| Byonic | Mass Spectronomy | yes | Based on tandem mass spectrometry data Byonic provides sensitive and comprehensive peptide and protein identification. | Link | |
| CycloBranch | Mass Spectronomy | yes | CycloBranch is a de novo peptide identification engine for identification of nonribosomal peptides (NRPs) from MS/MS. Cyclic, branched and branch-cyclic NRPs can be identified. CycloBranch is based on a database of nonribosomal building blocks which currently contains 287 annotated monomers (521 monomers including isomers). CycloBranch supports several file formats of peak lists (mzML and mzXML (requires OpenMS 1.11 installed), mgf (Mascot generic format), txt (containing a tab-separated m/z ratio and intensity on each line) and baf (a native file format of the manufacturer Bruker Daltonics; requires CompassX-Port 3.0 installed). The program has a graphical user interface. | Link | |
| PhosFox | Mass Spectronomy | yes | PhosFox enables peptide-level processing of phosphoproteomic data generated by multiple protein identification search algorithms (e.g. Mascot, Sequest, and Paragon) as well as cross-comparison of their identification results. The software supports both qualitative and quantitative phosphoproteomics studies, as well as multiple between-group comparisons. | Link | |
| DIA-Umpire | Mass Spectronomy | yes | DIA-Umpire analyses of data independent acquisition (DIA) mass spectrometry-based proteomics data. DIA-Umpire enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation. | Link | |
| Clique Enrichment Analysis for Proteomics | Mass Spectronomy | yes | Clique Enrichment Analysis for Proteomics serves as a protein interaction network-assisted approach to improve protein identification in shotgun proteomics. The thought process behind the method is that proteins eliminated as a result of insufficient experimental evidence are more likely to be present in the original sample if they exist in a clique enriched with confidently identified proteins. | Link | |
| Skyline | Mass Spectronomy | yes | Skyline builds selected reaction monitoring (SRM)/multiple reaction monitoring (MRM), parallel reaction monitoring (PRM - targeted MS/MS), data independent acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data. Skyline aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale proteomics studies. | Link | |
| OpenMS | Mass Spectronomy | yes | OpenMS emplyos an algorithm to align LC-MS samples and to match corresponding ion species across samples. | Link |
Tools for Mass Cytometry
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| CytofKit | Masscytometry | yes | An integrated mass cytometry data analysis pipeline that enables simultaneous illustration of cellular diversity and progression. Cytofkit firstly performs data pre-processing, and enables combined analysis of multiple Flow Cytometry Standard (FCS) files followed by data visualization, identifying cell subpopulations and detecting cellular progression. Cytofkit provides a graphical user interface for simplified usage. | Link | |
| FlowSOM | Masscytometry | yes | Analyzes flow or mass cytometry data using a self-organizing map. Using a two-level clustering and star charts, FlowSOM helps to obtain a clear overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. The algorithm consists of four steps: reading the data, building a self-organizing map, building a minimal spanning tree and computing a meta-clustering. Several visualization available: star charts to inspect several markers, pie charts to compare with manual gating results, variable node sizes dependent on the amount of cells assigned to the node and a grid or a tree structure which both give topological information. | Link |
Tools for Metagenomics
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| CoMet | Metagenomics | yes | The CoMet-Universe assists you in analyzing the taxonomic and functional composition of your metagenomic sample and to compare it with a large collection of publicly available data from previous metagenome studies. | Link |
Tools for Microarray
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| MarVis | Microarray | yes | The MarVis-Suite is a toolbox for filtering, combination, clustering, visualization, and functional analysis of Metabolic Markers, e.g. obtained from mass spectrometry (MS), microarray, or RNA-seq experiments. Additionally, the MarVis-Suite is able to adduct and isotope correction, molecular formula calculation, and pathway reconstruction based on accurate masses. | Link | |
| Venny 2,1 | Microarray | yes | Venny 2,1 is an interactive tool for comparing lists with Venn Diagrams. | Link | |
| BioVenn | Microarray | yes | BioVenn is a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. | Link | |
| Genevestigator | Microarray | yes | Genevestigator helps you interpret your results, prioritize targets and biomarkers, identify correlated genes, discover novel disease-specific genes, or simply to explore the world's gene expression data. The search engine processes measurement data from 17 organisms. | Link | |
| ASCAT | Microarray | yes | ASCAT is a tool for accurate dissection of genome-wide allele-specific copy number in tumors. ASCAT accounts for normal cell admixture and tumor aneuploidy in the analysis of SNP array data from cancer samples. ASCAT allows analysis of Illumina and Affymetrix SNP array data of tumor samples (with or without matching germline samples). | Link |
PCR Tools
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| PrimerX | PCR | yes | PrimerX designs PCR primers for site-directed mutagenesis. PrimerX compares a template DNA sequence with a DNA or protein sequence that already incorporates the desired mutation. It then generates forward primer sequences of appropriate length that encode this mutation based on your input. Finally, PrimerX generates corresponding reverse primer sequences, and gives you additionally information needed such as melting temperature and GC content for each primer pair. | Link | |
| GetPrime | PCR | yes | GetPrime designs high-quality primer pairs that can be used simultaneously to detect multiple target genes in qPCR experiments. | Link | |
| MRPrimerW | PCR | yes | MRPrimerW freely adjust filtering constraints, performing complete homology tests, supporting batch designing for qPCR as well as TaqMan probe design and ranking of primers. | Link | |
| VisualOMP | PCR | yes | VisualOMP designs several PCR primer for your desired conditions even in the presence of your existing oligo sets. The program features PCR Primer for standard PCR, Taqman, single- or multiplexed assay, SNP design, analyzing assays and micro arrays. | Link | |
| PCRdrive | PCR | yes | PCRdrive can find a PCR with all relevant informations among publicly available PCRs into the database, but also assists in the design of primers. By sharing PCRs you enable collaboration between researchers and help to grow the database. | Link | |
| CEMAsuite | PCR | yes | CEMAsuite constructs a codon-equivalent multiple alignment (CEMA) from a protein multiple sequence alignment (MSA) file, generate and score each position in the consensus DNA sequence using multiple algorithms, estimate the stability of degenerate primers on each of the coding sequences and design single-degeneracy primer backbones using Primer3. | Link | |
| Single Cell Expression Visualiser SCExV | PCR | yes | SCExV supports you in analyzing single cell qRT-PCR data. The program can import, filter, analyse, and visualise single cell gene expression data whilst being able to simultaneously consider cellular immunophenotype. SCExV is designed to be intuitive to use whilst maintaining advanced functionality and flexibility in how analyses are performed. | Link |
Tools for Proteomics
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| Predict Protein | Proteomics | yes | PredictProtein unites several features to characterize proteins such as prediction for secondary structure, transmembrane helices, protein-protein and protein-DNA binding sites, cysteine bonds, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, sub-cellular localization, domain boundaries, beta-barrels, metal binding sites, disulphide bridges, solvent accessibility. | Link | |
| PEAKS CMD | Proteomics | yes | The de novo sequencing software PEAKS can be used to study unsequenced organisms and indentify novel peptides. PEAKS has been mentioned by multiple independant publications as the best-performing de novo sequencing software. | Link | |
| PEAKS Studio | Proteomics | yes | PEAKS Studio combines De novo sequencing, protein identification, multi-engine protein identification, PTM search, sequence homology searching and quantification. | Link | |
| PANTHER-PSEP | Proteomics | yes | Panther-PSEP identifies single nucleotide polymorphism and estimates the likelihood of a particular amino-acid changing coding SNP to cause a functional impact on the protein. | Link | |
| SIFT | Proteomics | yes | SIFT predicts based on sequence homology and the physical properties of amino acids whether an amino acid substitution affects protein function. | Link | |
| MutationTaster | Proteomics | yes | MutationTaster estimates disease-causing potential of sequence alterations. | Link | |
| MuPIT | Proteomics | yes | MuPIT visualizes mutations on 3D structures. | Link | |
| LS-SNP | Proteomics | yes | LS-SNP/PDB provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological function. | Link | |
| PeCop | Proteomics | yes | PSI-BLAST your sequence to find Persistently Conserved Positions. | Link | |
| Rosetta | Proteomics | yes | The main features of the Rosetta Software include modeling and analysis of protein structures. Furthermore it supports de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. | Link |
Tools for Sequence Alignment
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| STRAP | Sequence Alignment | yes | STRAP combines useful tools for protein analysis. It can be used to generate and refine multiple alignments, to download PDB files from public ftp servers, visualize protein structural data with plugin or integrated protein structure viewers, and to map mutations onto three dimensional protein structures. You are able to load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs. | Link | |
| ConSurf | Sequence Alignment | yes | The ConSurf server estimates the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences. The conservation analysis of positions among members from the same family can often reveal the importance of each position for the protein (or nucleic acid)'s structure or function. One of the advantages of ConSurf in comparison to other methods is the accurate computation of the evolutionary rate by using either an empirical Bayesian method or a maximum likelihood (ML) method. | Link |
Tools for Transcriptomics
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| SpliceSeq | Transciptomics | yes | SpliceSeq investigates alternative mRNA splicing in next generation mRNA sequence data. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. | Link |
Data Management
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| labfolder | Data management | yes | labfolder is an electronic lab notebook that enables researchers to record findings and make new discoveries. By reinventing the traditional paper lab notebook, theproductivity & collaboration platform makes it easier to create, find, share, discuss & validate research data as a team. Therefore, labfolder accelerates the workflow and facilitates collaboration across the lab. | Link |
Diverse Softwares & Tools
| Software / Tool | Category | Free | FreeTrial | Tool Description | Link |
|---|---|---|---|---|---|
| PEAKS AB | Diverse | yes | PEAKS AB automates the sequencing process of antibody with LC-MS/MS or validates sequences of known antibodies. Furthermore modification and sequence variants can be quantified. | Link | |
| Align-GVGD | Diverse | yes | Align-GVGD predicts missense substitutions in genes of interest and whether they fall in a spectrum from enriched delterious to enriched neutral. The programm uses biophysical characteristics of amino acids aswell as protein multiple sequence alignments. | Link | |
| BLAT | Diverse | yes | BLAT on DNA finds similar sequences (25 bp and more) which match to at least 95%. BLAT on Proteins finds similar sequences (20 aa and more) which match to at least 80%. | Link | |
| FirstGlance in Jmol | Diverse | yes | FirstGlance in Jmol visualizes 3D structures of proteins, DNA, RNA, and their complexes. It is designed to see the main features of newly published 3D models in a few clicks. | Link | |
| Atlas of Macromolecules | Diverse | yes | Atlas contains about 160 extensively illustrated macromolecular 3D-structures with detailed background information. | Link | |
| Sequence Manipulation Suite | Diverse | yes | The Sequence Manipulation Suite is a collection of small programs for generating, formatting, and analyzing short DNA and protein sequences. | Link | |
| Savvy | Diverse | yes | Savvy is a plasmid drawing software that generates plasmid map in Scalable Vector Graphics format | Link | |
| Sequence Extractor | Diverse | yes | Sequence Extractor generates a clickable restriction map and PCR primer map of a DNA sequence. Protein translations and intron/exon boundaries are also shown. Use Sequence Extractor to build DNA constructs in silico. | Link | |
| EMBL | Diverse | yes | The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular databases. More than 40 different databases cover different fields like DNA&RNA, gene expression, proteins, structures, system and more. Additonally a varierty of tools are available. | Link |
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