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http://www.genoviewer.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data.

Proper citation: GenoViewer (RRID:SCR_001203) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/somaticcall-manual

Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.

Proper citation: SomaticCall (RRID:SCR_001196) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/peakanalyzer/wiki/

A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.

Proper citation: PeakAnalyzer (RRID:SCR_001194) Copy   

•   Source: SciCrunch Registry

http://ishtar.sourceforge.net/

A program for designing primer pairs that amplify multiple target sequences using DNA thermodynamics and one class support vector machines. Written in Python.

Proper citation: Ishtar (RRID:SCR_000538) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/denovogear/

A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations.

Proper citation: DeNovoGear (RRID:SCR_000670) Copy   

•   Source: SciCrunch Registry

http://functionalbio.com/web/

A service that provides low cost DNA sequencing. They utilize microfluidic technology.

Proper citation: Functional Biosciences (RRID:SCR_000943) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/

Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.

Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/igblast/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine.

Proper citation: IgBLAST (RRID:SCR_002873) Copy   

•   Source: SciCrunch Registry

http://clones.invitrogen.com/cloneranger.php

The Invitrogen Clone Collection: * Ultimate ORF Clones: Full-insert sequenced human and mouse open reading frames (ORFs) in a Gateway entry vector offering the highest utility for your downstream analysis needs. * GeneStorm Clones: GeneStorm Clones are human ORFs cloned and tested for expression in a mammalian, insect, or bacterial expression system. They are sequenced for identity and classification and are not guaranteed at the nucleotide level. * Full-Length Clones: An unparalleled repository of clones enriched for full-length inserts, derived from both public and proprietary sources. * BAC/PAC Clones: Invitrogen offers several genomic libraries from a selection of tissues and sources to facilitate your research and discovery. These collections are available in a variety of formats including clones, plates, pools and high-density colony membrane filters. * Yeast Deletions: Each yeast deletion represents a unique gene-knockout of the S. cerevisiae genome. Each open reading frame is knocked out using a PCR-based gene deletion strategy. Yeast deletions are available as clones, pools, plates and complete collections. * Yeast GFP Clones: The Yeast GFP Clone Collection of S. cerevisiae tagged open reading frames were generated by Dr. Erin O''Shea and Dr. Jonathan Weissman at University of California-San Francisco. The GFP fusion proteins are integrated into the yeast chromosome through homologous recombination and are expressed using endogenous promoters.

Proper citation: Invitrogen Clones (RRID:SCR_005371) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/a/blueprint.org/trades/

With Trajectory Directed Ensemble Sampling (TraDES) create large ensembles of high-quality protein structures quickly, ranging from near-native to partially unfolded to intrinsically unfolded. TraDES is a system for directly controlling and sampling protein conformational space. TraDES has been previously used for measuring the vastness of protein conformational space and testing the hypothesis of a brute force solution to the protein folding problem. Over 10 Billion protein structures have been produced by TraDES software in previous distributed computing experiments. The package is comprised of binary executable programs and accessory programs and scripts as well as protein structure data files that map out protein conformational space in a probabilistic way. The main programs are: * trades - generates protein structures following the Trajectory Distribution (see below) * seq2trj - makes Trajectory Distributions from sequences for sampling * str2tr - makes Trajectory Distributions from 3D structures for sampling Trajectory Distributions - Controlling the Sampling of Conformational Space The concept of the trajectory distribution may be new to many protein scientists. A trajectory distribution is simply a map of available conformational space at an amino acid residue. NMR scientists are the primary users of the TraDES package.

Proper citation: TraDES (RRID:SCR_006142) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/sites/batchentrez

Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers.

Proper citation: Batch Entrez (RRID:SCR_016634) Copy   

•   Source: SciCrunch Registry

http://www.bondxray.org/software/aline.html

Software interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Extensible WYSIWYG protein sequence alignment editor for publication quality figures.

Proper citation: Aline (RRID:SCR_016886) Copy   

•   Source: SciCrunch Registry

https://github.com/kblin/merge-gbk-records

Software tool to merge multiple GenBank records using defined spacer sequence.Used to turn multiple GenBank records either in multiple files or single multi-record file into single record.

Proper citation: merge-gbk-records (RRID:SCR_017968) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/nast

A knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on: 1. primary sequence 2. known or predicted secondary structure 3. known or predicted tertiary contacts (optional) Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures. NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data. Imported from BiositeMaps registry

Proper citation: NAST (RRID:SCR_006995) Copy   

•   Source: SciCrunch Registry

http://tree.bio.ed.ac.uk/software/seqgen/

Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.

Proper citation: Seq-Gen (RRID:SCR_014934) Copy   

•   Source: SciCrunch Registry

http://www.jstacs.de/index.php/GeMoMa

Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species.

Proper citation: GeMoMa (RRID:SCR_017646) Copy   

•   Source: SciCrunch Registry

http://www.uwstructuralgenomics.org/

It is a specialized research center supported by the Protein Structure Initiative (PSI) of the National Institute of General Medical Sciences (NIGMS), one of the National Institutes of Health (NIH). PSI is a federal, university, and industry effort aimed at dramatically reducing the costs and lessening the time it takes to determine a three-dimensional protein structure. The long-range goal of PSI is to solve 10,000 protein structures in 10 years and to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. CESG is located within the Department of Biochemistry at the University of Wisconsin-Madison (Madison, WI) and the Department of Biochemistry at the Medical College of Wisconsin (Milwaukee, WI). CESG develops new methods and technologies to address unique eukaryotic bottlenecks and disseminates its methodologies and experimental results to the scientific community worldwide through: :- Cell-Free Protein Production Workshops :- Plasmids at PSI Materials Repository :- Posters Presented at Scientific Meetings :- Publications in PubMed / PubMed Central :- Sesame (LIMS) Available for Researchers :- Solved Structures in the Protein Data Bank :- Technology Dissemination Reports They have welcomed requests by researchers to solve eukaryotic protein structures, particularly medically relevant proteins, through our Online Structure Request System for Researchers. They have solved many community-nominated targets and deposited information about these targets in public databases and published on our investigations and findings. Sponsors: CESG is supported by NIH / NIGMS Protein Structure Initiative grant numbers U54 GM074901 and P50 GM064598.

Proper citation: CESG (RRID:SCR_008451) Copy   

•   Source: SciCrunch Registry

http://www.ccb.jhu.edu/

Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis.

Proper citation: Center for Computational Biology at JHU (RRID:SCR_016680) Copy   

•   Source: SciCrunch Registry

http://humancyc.org/

The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version.

Proper citation: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) Copy   

•   Source: SciCrunch Registry

http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi

Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GOblet (RRID:SCR_006998) Copy   

•   Source: SciCrunch Registry