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http://www.timelogic.com/catalog/799/velocimapper

Accelerated alignment tool for mapping data from next-generation DNA sequencing systems. It runs on TimeLogic''s newest FPGA-based DeCypher J-Series Similarity Search Engine Accelerator to provide fast and reliable results that significantly outperform software-only or GPU-accelerated alternatives.

Proper citation: VelociMapper (RRID:SCR_005262) Copy   

•   Source: SciCrunch Registry

http://linux1.softberry.com/spldb/SpliceDB.html

Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.

Proper citation: SpliceDB (RRID:SCR_006262) Copy   

•   Source: SciCrunch Registry

http://www.pathxl.com/pathxl-research/pathxl-tma

Tissue microarray (TMA) Software used for Biomarker Discovery that allows TMA experiments to be performed anytime, anywhere, reducing administrative costs and time. It is designed to support TMA scoring workflow and allows configuration of experiments in minutes. Access and view clinical metadata, the TMA core, scoring criteria and the TMA map all on a single interface.

Proper citation: PathXL TMA (RRID:SCR_005596) Copy   

•   Source: SciCrunch Registry

http://www.dnabaser.com/download/chromatogram-explorer/

A Windows Explorer clone dedicated to DNA sequence analysis and manipulation. View, edit, and convert chromatograms. Trim low quality ends automatically. The Lite version of Chromatogram Explorer is freeware.

Proper citation: DNA Chromatogram Explorer (RRID:SCR_005585) Copy   

•   Source: SciCrunch Registry

http://abi.inf.uni-tuebingen.de/Services/YLoc/webloc.cgi

An interpretable web server for predicting subcellular localization. In addition to the predicted location, YLoc gives a reasoning why this prediction was made and which biological properties of the protein sequence lead to this prediction. Moreover, a confidence estimate helps users to rate predictions as trustworthy. YLoc+ is able to predict the location of multiple-targeted proteins with high accuracy. The YLoc webserver is also accessible via SOAP.

Proper citation: YLoc (RRID:SCR_002464) 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

https://www.biodiscovery.com/search/node?keys=Imagene

Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ImaGene (RRID:SCR_002178) Copy   

•   Source: SciCrunch Registry

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

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://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://bioconductor.org/packages/2.8/bioc/html/qrqc.html

Software R package to quickly scan reads and gather statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.

Proper citation: qrqc (RRID:SCR_006867) 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://sourceforge.net/projects/hadoop-bam/

A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF.

Proper citation: Hadoop-BAM (RRID:SCR_005516) 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://htseq.readthedocs.io/en/release_0.9.1/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.

Proper citation: HTSeq (RRID:SCR_005514) 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