Tools   Select Another Resource Report Type

http://cbrc.kaust.edu.sa/readscan/

A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.

Proper citation: READSCAN (RRID:SCR_005204) Copy   

•   Source: SciCrunch Registry

http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html

An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input.

Proper citation: VirusSeq (RRID:SCR_005206) Copy   

•   Source: SciCrunch Registry

http://snpeff.sourceforge.net/

Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs.

Proper citation: SnpEff (RRID:SCR_005191) Copy   

•   Source: SciCrunch Registry

http://phast.wishartlab.com/

A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available.

Proper citation: PHAge Search Tool (RRID:SCR_005184) Copy   

•   Source: SciCrunch Registry

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

A simple and easy to use high through-put analysis tool which can provide comprehensive annotation of both novel and known single nucleotide polymorphisms (SNPs) for any organism with a draft sequence and annotation. SNPdat makes possible analyses involving non-model organisms that are not supported by the vast majority of SNP annotation tools currently available. It is especially intended for use by researchers with limited bioinformatic experience.

Proper citation: SNPdat (RRID:SCR_005187) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/clever-sv/

A collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python.

Proper citation: CLEVER Toolkit (RRID:SCR_005255) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/clippers/

A software program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads. Currently, Clippers is implemented for long reads Illumina, ex: 75bp or 100bp, allowing mismatches and a single deletion/splicing. Clippers is a sister tool of PerM, our short reads aligner. Users are strongly suggested to use PerM to initially mapped reads and identify the deletion/splicing with the initially unmapped reads. We plan to extend it to ABI SOLiD reads in the near future. Clippers outputs gap-alignments in SAM format. You can use SAMtools or other program to interpret the deletion/splicing. The input files are a reference in fasta format and the reads is in fasta or fastq format.

Proper citation: Clippers (RRID:SCR_005256) Copy   

•   Source: SciCrunch Registry

http://sv.gersteinlab.org/age/

A tool that implements an algorithm for optimal alignment of sequences with Structural Variations (SVs).

Proper citation: AGE (RRID:SCR_005253) Copy   

•   Source: SciCrunch Registry

http://skatebase.org/

Portal supporting the North East Bioinformatics Collaborative''s project to sequence the genome of the Little Skate. Provided is a clearinghouse for Little Skate Genome Project and other publicly available Skate and Ray (Batoidea) genome data, and tools for data visualization and analysis. Little Skate Genome Project The little skate (Leucoraja erinacea) is a chondrichthyan (cartilaginous) fish native to the east coast of North America. Elasmobranchs (Skates, Rays, and Sharks) exhibit many fundamental vertebrate characteristics, including a neural crest, jaws and teeth, an adaptive immune system, and a pressurized circulatory system. These characteristics have been exploited to promote understanding about human physiology, immunology, stem cell biology, toxicology, neurobiology and regeneration. The development of standardized experimental protocols in elasmobranchs such as L. erinacea and the spiny dogfish shark (Squalus acanthias) has further positioned these organisms as important biomedical and developmental models. Despite this distinction, the only reported chondrichthyan genome is the low coverage (1.4x) draft genome of the elephant shark (Callorhinchus milii). To close the evolutionary gaps in available elasmobranch genome sequence data, and generate critical genomic resources for future biomedical study, the genome of L. erinacea is being sequenced by the North East Bioinformatics Collaborative (NEBC). As close evolutionary relatives, the little skate sequence will facilitate studies that employ dogfish shark and other elasmobranchs as model organisms. Skate tools include the SkateBLAST and the Skate Genome Browsers: Little Skate Mitochondrion, Thorny Skate Mitochondrion, and Ocellate Spot Skate Mitochondrion.

Proper citation: SkateBase (RRID:SCR_005302) Copy   

•   Source: SciCrunch Registry

http://ingap.sourceforge.net/

Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations.

Proper citation: inGAP (RRID:SCR_005261) Copy   

•   Source: SciCrunch Registry

http://sv.gersteinlab.org/pemer/

Software package as computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from novel genome.

Proper citation: PEMer (RRID:SCR_005263) Copy   

•   Source: SciCrunch Registry

http://en.wikipedia.org/wiki/Gene_Wiki

The Gene Wiki is a project that facilitates transferring information on human genes to Wikipedia article stubs with the goal of promoting collaboration and expansion of the articles. Number of gene articles The human genome contains an estimated 20,00025,000 protein-coding genes. The goal of the Gene Wiki project is to create seed articles for every notable human gene, that is, every gene whose function has been assigned in the peer-reviewed scientific literature. Approximately half of human genes have assigned function, therefore the total number of articles seeded by the Gene Wiki project would be expected to be in the range of 10,000 - 15,000. To date, approximately 10,271 articles have been created or augmented to include Gene Wiki project content. Expansion Once seed articles have been established, the hope and expectation is that these will be annotated and expanded by editors ranging in experience from the lay audience to students to professionals and academics. Proteins encoded by genes The majority of genes encode proteins hence understanding the function of a gene generally requires understanding of the function of the corresponding protein. In addition to including basic information about the gene, the project therefore also includes information about the protein encoded by the gene. Stubs for the Gene Wiki project are created by a bot and contain links to the following primary gene/protein databases * HUGO Gene Nomenclature Committee official gene name * Entrez Gene database * OMIM (Mendelian Inheritance in Man) database that catalogues all the known diseases with a genetic component * Amigo Gene Ontology * HomoloGene gene homologs in other species * SymAtlasRNA gene expression pattern in tissues * Protein Data Bank 3D structure of protein encoded by the gene * Uniprot (universal protein resource) a central repository of protein data

Proper citation: Gene Wiki (RRID:SCR_005317) Copy   

•   Source: SciCrunch Registry

http://dna.cs.byu.edu/gnumap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions.

Proper citation: GNUMAP (RRID:SCR_005482) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cushaw2/files/CUSHAW2-GPU/

Software program (based on CUSHAW2) designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones.

Proper citation: CUSHAW2-GPU (RRID:SCR_005480) Copy   

•   Source: SciCrunch Registry

http://mbgd.genome.ad.jp/CGAT/

A comparative genome analysis tool for detailed comparison of closely related bacterial-sized genomes. It visualizes precomputed pairwise genome alignments on both dotplot and alignment viewers. Users can add information on this alignment, such as existence of tandem repeats or interspersed repetitive sequences and changes in codon usage bias, to facilitate interpretation of the observed genomic changes. Besides visualization functionalities, it also provides a general framework to process genome-scale alignments using various existing alignment programs. CGAT employs a client-server architecture, which consists of AlignmentViewer (client; a Java application) and DataServer (a set of Perl scripts). The DataServer package contains data construction scripts and CGI scripts and the AlignmentViewer program visualizes the alignment data obtained from the server thorough the HTTP protocol.

Proper citation: CGAT (RRID:SCR_005550) Copy   

•   Source: SciCrunch Registry

http://cushaw2.sourceforge.net/homepage.htm#latest

Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome.

Proper citation: CUSHAW (RRID:SCR_005479) Copy   

•   Source: SciCrunch Registry

http://manatee.sourceforge.net/

Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris

Proper citation: Manatee (RRID:SCR_005685) Copy   

•   Source: SciCrunch Registry

http://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/lookseq/

A web-based application for alignment visualization, browsing and analysis of genome sequence data.

Proper citation: LookSeq (RRID:SCR_005625) Copy   

•   Source: SciCrunch Registry

http://hadvwg.gmu.edu/

The Human Adenovirus Type Classification coordinates the naming of candidate new types, prior to manuscript submission for peer review. This resource contains a method of submitting candidate HAdV, criteria for a new HAdV type, and a Serotyping tool, which displays all potential types corresponding to the query serotype entered by a user. The criteria are based on discussions at the International Adenovirus Meeting (Dobog��k, Hungary; 26-30 April, 2009) and the NIH Human Adenovirus Working Group Workshop (Bethesda, MD. USA; 3 February 2011), which are summarized in a Letter to the Editor.

Proper citation: Human Adenovirus Type Classification (RRID:SCR_005753) Copy   

•   Source: SciCrunch Registry