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Databases and portal to data and ordering mouse strains from MRC Harwell including mouse stocks in FESA (Frozen Embryo and Sperm Archive), mutants from the mutagenesis screen, the ENU DNA archive, standardized phenotyping procedures, imprinting genes and chromosome anomalies. The portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide added value information above and beyond what is available through other routes such as IMSR (International Mouse Stain Resource). MouseBook can be searched either using an intuitive Google-style free text search or using the Mammalian Phenotype Ontology (MP) tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database. Results are returned in a tabbed format providing categorized results identified from each of the catalogs in MouseBook. Individual results lines from each catalog include information on gene, allele, chromosomal location and phenotype and provide a simple click-through link to further information as well as ordering the strain. The infrastructure underlying MouseBook has been designed to be extensible, allowing additional data sources to be added enabling other sites to make their data directly available through MouseBook.
Proper citation: MouseBook (RRID:SCR_006358) Copy
https://bioconductor.org/packages/IRanges/
Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible.
Proper citation: IRanges (RRID:SCR_006420) Copy
http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna
A de novo assembly program targeting populations with high mutation rates.
Proper citation: VICUNA (RRID:SCR_006302) Copy
https://github.com/ding-lab/msisensor
A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.
Proper citation: MSIsensor (RRID:SCR_006418) Copy
http://www.clipz.unibas.ch/downloads/TSSer/index.php
A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide.
Proper citation: TSSer (RRID:SCR_006419) Copy
FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain.
Proper citation: Flycircuit (RRID:SCR_006375) Copy
Forum for researchers in human developmental biology and related fields to meet and establish links.
Proper citation: HUDSEN (RRID:SCR_006324) Copy
https://github.com/HIITMetagenomics/dsm-framework
Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples.
Proper citation: Distributed String Mining Framework (RRID:SCR_004736) Copy
https://tobiasrausch.com/delly/
Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome.
Proper citation: DELLY (RRID:SCR_004603) Copy
http://cran.r-project.org/web/packages/kdetrees/
R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.
Proper citation: Kdetrees (RRID:SCR_004522) Copy
http://noble.gs.washington.edu/proj/philius/
Web server that predicts protein transmembrane topology and signal peptides. Hidden Markov models (HMM) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. They expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBN). Their model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide sub-model with a transmembrane sub-model. They introduce a two-stage DBN decoder which combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions.
Proper citation: Philius (RRID:SCR_004625) Copy
http://metaphyler.cbcb.umd.edu/
A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database.
Proper citation: MetaPhyler (RRID:SCR_004848) Copy
This collection of software is designed to rapidly identify identifies primer and microarray probe binding sites for a query sequence in genomic DNA. This software suite has four main programs:1. A program for indexing a sequence file to speed up the binding site search. 2. A program for retrieving the binding sites of a query sequence. 3. A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence 4. A program for analyzing a set of binding sites to tailor the search for different reaction conditions. This software is implemented in C.
Proper citation: hyfi: software suite for binding site search (RRID:SCR_004884) Copy
http://huttenhower.sph.harvard.edu/metaphlan2
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes.
Proper citation: MetaPhlAn (RRID:SCR_004915) Copy
A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.
Proper citation: USeq (RRID:SCR_004753) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi
Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.
Proper citation: NCBI BLAST (RRID:SCR_004870) Copy
http://ibis.tau.ac.il/miRNAkey/
A software pipeline for the analysis of microRNA Deep Sequencing data.
Proper citation: miRNAKey (RRID:SCR_004813) Copy
http://svmerge.sourceforge.net/
Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.
Proper citation: SVMerge (RRID:SCR_004777) Copy
http://www.engr.uconn.edu/~jiz08001/svseq2.html
Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions.
Proper citation: SVseq (RRID:SCR_004804) Copy
A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
Proper citation: Minia (RRID:SCR_004986) Copy
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