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http://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
http://biodoop-seal.sourceforge.net/
A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.
Proper citation: SEAL (RRID:SCR_010914) Copy
http://cran.r-project.org/web/packages/DIME/index.html
R-package for identifying differential ChIP-seq based on an ensemble of mixture models.
Proper citation: DIME (RRID:SCR_010874) Copy
http://bio-bwa.sourceforge.net/
Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
Proper citation: BWA (RRID:SCR_010910) Copy
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
Proper citation: CloudBurst (RRID:SCR_010911) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.
Proper citation: T1DBase (RRID:SCR_007959) Copy
http://www.ebi.ac.uk/huber-srv/hilbert/
Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features.
Proper citation: HilbertVis (RRID:SCR_007862) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
https://www.ncbi.nlm.nih.gov/genbank/dbest/
Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
Proper citation: dbEST (RRID:SCR_008132) Copy
http://erlichlab.wi.mit.edu/lobSTR/
A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: lobSTR (RRID:SCR_008030) Copy
http://www.baderlab.org/Software/ActiveDriver
A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications.
Proper citation: ActiveDriver (RRID:SCR_008104) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.
Proper citation: QIIME (RRID:SCR_008249) Copy
http://bioinfo.cipf.es/isacghtrac
Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.
Proper citation: IsaCGH (RRID:SCR_008375) Copy
Griffin (G-protein-receptor interacting feature finding instrument) is a high-throughput system to predict GPCR - G-protein coupling selectively with the input of GPCR sequence and ligand molecular weight. This system consists of two parts: 1) HMM section using family specific multiple alignment of GPCRs, 2) SVM section using physico-chemical feature vectors in GPCR sequence. G-protein coupled receptors (GPCR), which is composed of seven transmembrane helices, play a role as interface of signal transduction. The external stimulation for GPCR, induce the coupling with G-protein (Gi/o, Gq/11, Gs, G12/13) followed by different kinds of signal transduction to inner cell. About half of distributed drugs are intending to control this GPCR - G-protein binding system, and therefore this system is important research target for the development of effective drug. For this purpose, it is necessary to monitor, effectively and comprehensively, of the activation of G-protein by identifying ligand combined with GPCR. Since, at present, it is difficult to construct such biochemical experiment system, if the answers for experimental results can be prepared beforehand by using bioinformatics techniques, large progress is brought to G-protein related drug design. Previous works for predicting GPCR-G protein coupling selectivity are using sequence pattern search, statistical models, and HMM representations showed high sensitivity of predictions. However, there are still no works that can predict with both high sensitivity and specificity. In this work we extracted comprehensively the physico-chemical parameters of each part of ligand, GPCR and G-protein, and choose the parameters which have strong correlation with the coupling selectivity of G-protein. These parameters were put as a feature vector, used for GPCR classification based on SVM.
Proper citation: G protein receptor interaction feature finding instrument (RRID:SCR_008343) Copy
http://tree.bio.ed.ac.uk/software/figtree
A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.
Proper citation: FigTree (RRID:SCR_008515) Copy
http://biosig.sourceforge.net/
Software library for processing of electroencephalogram (EEG) and other biomedical signals like electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis. Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis. It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events.
Proper citation: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis (RRID:SCR_008428) Copy
http://mothra.ornl.gov/cgi-bin/cat/cat.cgi
A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CAT (RRID:SCR_008421) Copy
http://bioinf.uni-greifswald.de/augustus/
Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.
Proper citation: Augustus (RRID:SCR_008417) Copy
http://www.sailing.cs.cmu.edu/main/?page_id=511
Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns.
Proper citation: SPEX2 (RRID:SCR_014923) Copy
https://dogma.ccbb.utexas.edu/
Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
Proper citation: DOGMA (RRID:SCR_015060) Copy
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