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http://www.tc.umn.edu/~konox006/Code/SNPMeta/

A Python and BioPython-based tool to generate metadata for single nucleotide polymorphisms (SNPs) for easy filtering, or submission to SNP databases. Information reported includes gene name, whether the SNP is coding or noncoding, and whether the SNP is synonymous or nonsynonymous. SNPMeta outputs in either a dbSNP submission report format, or a tab-delimited format. There is a also Web-based version available that only annotates with default settings, and only annotates a maximum of 20 SNPs at one time. The script may be downloaded for full functionality.

Proper citation: SNPMeta (RRID:SCR_002005) Copy   

•   Source: SciCrunch Registry

https://github.com/ndaniel/fusioncatcher

Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

Proper citation: FusionCatcher (RRID:SCR_000060) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.nl/QualitySNPng/

Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy.

Proper citation: QualitySNPng (RRID:SCR_002479) Copy   

•   Source: SciCrunch Registry

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

Software that simulates PacBio reads by using either a model-based or sampling-based simulation.

Proper citation: PBSIM (RRID:SCR_002512) Copy   

•   Source: SciCrunch Registry

http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/default.htm

Project to improve the microarray and next-generation sequencing technologies and foster their proper applications in discovery, development and review of FDA regulated products by developing standards and quality measures. Microarrays and next-generation sequencing represent core technologies in pharmacogenomics and toxicogenomics; however, before these technologies can successfully and reliably be used in clinical practice and regulatory decision-making, standards and quality measures need to be developed. Everyone is invited to participate in the MAQC project.

Proper citation: MAQC (RRID:SCR_002351) Copy   

•   Source: SciCrunch Registry

http://dissect-trans.sourceforge.net/Home

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

Proper citation: Dissect (RRID:SCR_000058) Copy   

•   Source: SciCrunch Registry

http://burgundy.cmmt.ubc.ca/cgi-bin/RAVEN/a?rm=home

Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RAVEN (RRID:SCR_001937) Copy   

•   Source: SciCrunch Registry

http://snpeffect.vib.be/

A database for phenotyping human single nucleotide polymorphisms (SNPs)that primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. They provide a detailed variant analysis using their tools such as: * TANGO to predict aggregation prone regions * WALTZ to predict amylogenic regions * LIMBO to predict hsp70 chaperone binding sites * FoldX to analyse the effect on structure stability Further, SNPeffect holds per-variant annotations on functional sites, structural features and post-translational modification. The meta-analysis tool enables scientists to carry out a large scale mining of SNPeffect data and visualize the results in a graph. It is now possible to submit custom single protein variants for a detailed phenotypic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SNPeffect (RRID:SCR_005091) Copy   

•   Source: SciCrunch Registry

http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl

A database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains >2000 samples from >500 ChIP-seq and ChIP-chip experiments, representing a total of >170 proteins and >10,000,000 protein-DNA interactions (March 2014). A web server provides an interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell type dependencies, and cross-sample variability of protein-DNA interactions.

Proper citation: hmChIP (RRID:SCR_005407) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/lib/chea.jsp

Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes.

Proper citation: ChEA (RRID:SCR_005403) Copy   

•   Source: SciCrunch Registry

http://www.patricbrc.org/portal/portal/patric/Home

A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.

Proper citation: Pathosystems Resource Integration Center (RRID:SCR_004154) Copy   

•   Source: SciCrunch Registry

http://regulondb.ccg.unam.mx/

Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.

Proper citation: RegulonDB (RRID:SCR_003499) Copy   

•   Source: SciCrunch Registry

http://sb.cs.cmu.edu/seecer/

Algorithm for sequencing error correction of RNA-seq data sets. SEECER removes mismatch and indel errors from the raw reads and improves downstream analysis of the data.

Proper citation: SEECER (RRID:SCR_005274) Copy   

•   Source: SciCrunch Registry

http://www.GeneWeaver.org

Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.

Proper citation: Gene Weaver (RRID:SCR_003009) Copy   

•   Source: SciCrunch Registry

http://genome.unmc.edu/ngLOC/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License.

Proper citation: ngLOC (RRID:SCR_003150) Copy   

•   Source: SciCrunch Registry

http://www.gene-talk.de

A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations.

Proper citation: GeneTalk (RRID:SCR_005231) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/minimap2

Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences.

Proper citation: Minimap2 (RRID:SCR_018550) Copy   

•   Source: SciCrunch Registry

http://jefferis.github.io/nat/

Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.

Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy   

•   Source: SciCrunch Registry

http://projects.biotec.tu-dresden.de/metapocket/

Software tool to identify pockets on protein surface to predict ligand-binding sites.

Proper citation: metaPocket (RRID:SCR_016653) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/fermi

Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.

Proper citation: fermi (RRID:SCR_016652) Copy   

•   Source: SciCrunch Registry