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

Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments.

Proper citation: Conserved Domain Database (RRID:SCR_002077) Copy   

•   Source: SciCrunch Registry

http://phylopythias.bifo.helmholtz-hzi.de/index.php?phase=wait

Web Server for Taxonomic Assignment of Metagenome Sequences that is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments.

Proper citation: PhyloPythiaS (RRID:SCR_011923) Copy   

•   Source: SciCrunch Registry

http://www.kazusa.or.jp/kaos/

This site has been developed by Kazusa DNA Research Institute for the purpose of offering the science community the analyzed sequence data produced by a multi-national Arabidopsis genome sequencing project coordinated by the Arabidopsis Genome Initiatives (AGI). The aim of this service is to enable users to browse the annotated sequence data produced by all the sequencing teams of AGI through an user-friendly graphic display system and search engines. Gene structures proposed on the annotated sequences as well as those predicted by computer programs are presented and each graphic item has a hyperlink to detailed information of the corresponding area. The nucleotide sequence data deposited in GenBank by AGI was downloaded, re-computer-analyzed at Kazusa and parsed results are displayed graphically.

Proper citation: Kazusa Arabidopsis data opening site (RRID:SCR_013511) Copy   

•   Source: SciCrunch Registry

http://mirwalk.umm.uni-heidelberg.de/

Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets.

Proper citation: miRWalk (RRID:SCR_016509) Copy   

•   Source: SciCrunch Registry

http://viewer.shigen.info/cgi-bin/crispr/crispr.cgi

Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.

Proper citation: NBRP Medaka CRISPR target site (RRID:SCR_018159) Copy   

•   Source: SciCrunch Registry

http://cisbp.ccbr.utoronto.ca

Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.

Proper citation: CIS-BP (RRID:SCR_017236) Copy   

•   Source: SciCrunch Registry

https://web.uri.edu/riinbre/mic/

Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research.

Proper citation: Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) Copy   

•   Source: SciCrunch Registry

http://mgm.ku.edu/services

Research oriented service laboratory providing informatics support to research community. Services include data analysis and mining in proteomics, genomics and chemistry, systems biology approaches such as pathway, network and interaction analyses, large scale statistical and machine learning studies, protein structure, function and stability prediction, sequence and domain analyses,d esign and implementation of relational databases and software programs, consultation on experimental design involving data acquisition, management and analysis, report, grant, and manuscript preparation.

Proper citation: Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility (RRID:SCR_017751) Copy   

•   Source: SciCrunch Registry

http://genetics.group.shef.ac.uk/index.html

Core provides DNA sequencing services including DNA extraction, cell line identification, microsatellite analysis, and antibody sequencing,DNA Sequencing, Monoclonal Antibody Sequencing,Nucleic Acid Quantification,PCR Machine Hire,Real-Time PCR Robotic Liquid Handling,Taqman SNP Analysis.

Proper citation: University of Sheffield Genomic Core Facility (RRID:SCR_017912) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/RNAmmer/

Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.

Proper citation: RNAmmer (RRID:SCR_017075) Copy   

•   Source: SciCrunch Registry

https://github.com/INTABiotechMJ/MITE-Tracker

Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.

Proper citation: MITE-Tracker (RRID:SCR_017030) Copy   

•   Source: SciCrunch Registry

https://github.com/ruanjue/wtdbg2.git

Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.

Proper citation: WTDBG (RRID:SCR_017225) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/psmc.git

Software package for implementation of Pairwise Sequentially Markovian Coalescent model. Infers population size history from diploid sequence.

Proper citation: PSMC (RRID:SCR_017229) Copy   

•   Source: SciCrunch Registry

http://wasabiapp.org/software/prank/

Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

Proper citation: prank (RRID:SCR_017228) Copy   

•   Source: SciCrunch Registry

https://github.com/josephryan/matemaker

Software tool to make artificial mate pairs from long sequences for scaffolding.

Proper citation: matemaker (RRID:SCR_017199) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/GraphClust-2

Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function.

Proper citation: GraphClust2 (RRID:SCR_017286) Copy   

•   Source: SciCrunch Registry

https://www.drive5.com/piler/

Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats.

Proper citation: PILER (RRID:SCR_017333) Copy   

•   Source: SciCrunch Registry

http://refgenie.databio.org

Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis.

Proper citation: refgenie (RRID:SCR_017574) Copy   

•   Source: SciCrunch Registry

http://heimanlab.com/cut2.html

Software tool to find restriction endonucleases. Helps restriction map nucleotide sequences. Tool with customizable interface, platform independent accessibility, interfaces to NCBI's GenBank, DNA sequence database, and NEB's REBase, and restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including option of finding restriction sites that can be introduced into sequence by silent mutagenesis.

Proper citation: Webcutter (RRID:SCR_017638) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SuperDCA

Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.

Proper citation: SuperDCA (RRID:SCR_018175) Copy   

•   Source: SciCrunch Registry