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http://chipster.csc.fi/

A user-friendly analysis software for high-throughput data.

Proper citation: Chipster (RRID:SCR_010939) Copy   

•   Source: SciCrunch Registry
  

http://plntfdb.bio.uni-potsdam.de

Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family.

Proper citation: PlnTFDB (RRID:SCR_010899) Copy   

•   Source: SciCrunch Registry
  

http://methmarker.mpi-inf.mpg.de/

Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser.

Proper citation: MethMarker (RRID:SCR_010908) Copy   

•   Source: SciCrunch Registry
  

http://sissrs.rajajothi.com/

Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.

Proper citation: SISSRs (RRID:SCR_010866) Copy   

•   Source: SciCrunch Registry
  

http://code.google.com/p/zinba/

Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.

Proper citation: ZINBA (RRID:SCR_010868) Copy   

•   Source: SciCrunch Registry
  

http://aroma-project.org/

An R package for analyzing large Affymetrix data sets.

Proper citation: Aroma.affymetrix (RRID:SCR_010919) Copy   

•   Source: SciCrunch Registry
  

http://kmersvm.beerlab.org/

A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.

Proper citation: kmer-SVM (RRID:SCR_010882) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.au.tsinghua.edu.cn/software/NURD/

An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NURD (RRID:SCR_010988) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/Tools/msa/kalign/

A fast and accurate multiple sequence alignment algorithm.

Proper citation: Kalign (RRID:SCR_011810) Copy   

•   Source: SciCrunch Registry
  

http://mafft.cbrc.jp/alignment/server/

Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.

Proper citation: MAFFT (RRID:SCR_011811) Copy   

•   Source: SciCrunch Registry
  

http://wishart.biology.ualberta.ca/cgview/

A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CGView (RRID:SCR_011779) Copy   

•   Source: SciCrunch Registry
  

http://bioen-compbio.bioen.illinois.edu/PSAR-Align/

Software for improving multiple sequence alignment using probabilistic sampling.

Proper citation: PSAR-Align (RRID:SCR_011814) Copy   

•   Source: SciCrunch Registry
  

http://gaggle.systemsbiology.net/docs/geese/genomebrowser/

An open source software tool for visualizing high-density data plotted against coordinates on the genome.

Proper citation: Gaggle (RRID:SCR_011780) Copy   

•   Source: SciCrunch Registry
  

https://bioinf.eva.mpg.de/patman/

Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PatMaN (RRID:SCR_011821) Copy   

•   Source: SciCrunch Registry
  

http://www.g-language.org/GenomeProjector/

A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.

Proper citation: Genome Projector (RRID:SCR_011790) Copy   

•   Source: SciCrunch Registry
  

https://gemini.readthedocs.io/en/latest/

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

Proper citation: GEMINI (RRID:SCR_014819) Copy   

•   Source: SciCrunch Registry
  

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

Proper citation: Bowtie 2 (RRID:SCR_016368) Copy   

•   Source: SciCrunch Registry
  

http://dgrapov.github.io/MetaMapR/

An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.

Proper citation: MetaMapR (RRID:SCR_014685) Copy   

•   Source: SciCrunch Registry
  

http://abacus.gene.ucl.ac.uk/software/paml.html

Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PAML (RRID:SCR_014932) Copy   

•   Source: SciCrunch Registry
  

http://regulatorygenomicsgroup.org/chicago

Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CHiCAGO (RRID:SCR_014941) Copy   

•   Source: SciCrunch Registry