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https://huygens.science.uva.nl/PlotTwist/

Web application for plotting and annotating continuous data. Open source web app for plotting and annotating time series data. Used to inspect data and generate publication quality visualizations. Available options for plotting include lineplot, small multiples and heatmap, summary statistics and inferential statistics.

Proper citation: PlotTwist (RRID:SCR_018331) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/CRISPRcasIdentifier

Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes.

Proper citation: CRISPRcasIdentifier (RRID:SCR_018296) Copy   

•   Source: SciCrunch Registry

https://www.sympy.org/en/index.html

Software Python library for symbolic mathematics. It aims to become full featured computer algebra system (CAS) while keeping code as simple as possible in order to be comprehensible and easily extensible.

Proper citation: SymPy (RRID:SCR_018417) Copy   

•   Source: SciCrunch Registry

https://github.com/smortezah/smashpp

Software tool to find and visualize rearrangements in DNA sequences.

Proper citation: smashpp (RRID:SCR_018307) Copy   

•   Source: SciCrunch Registry

http://sumosp.biocuckoo.org.

Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup.

Proper citation: GPS-SUMO (RRID:SCR_018261) Copy   

•   Source: SciCrunch Registry

https://github.com/xiaeryu/SpoTyping-v2.0

Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads.

Proper citation: SpoTyping (RRID:SCR_018466) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/minimap2

Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences.

Proper citation: Minimap2 (RRID:SCR_018550) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry

http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx

Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.

Proper citation: DAMBE (RRID:SCR_018528) Copy   

•   Source: SciCrunch Registry

https://www.epimodel.org/

Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.

Proper citation: EpiModel (RRID:SCR_018539) Copy   

•   Source: SciCrunch Registry

https://github.com/lmb-embrapa/machado

Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code.

Proper citation: Machado (RRID:SCR_018428) Copy   

•   Source: SciCrunch Registry

https://prosa.services.came.sbg.ac.at/prosa.php

Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling.

Proper citation: ProSA-web (RRID:SCR_018540) Copy   

•   Source: SciCrunch Registry

https://github.com/yanzhanglab/Graph2GO

Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology.

Proper citation: Graph2GO (RRID:SCR_018726) Copy   

•   Source: SciCrunch Registry

http://indel.bioinfo.sdu.edu.cn/gridsphere/gridsphere

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions.

Proper citation: IndelFR - Indel Flanking Region Database (RRID:SCR_006050) Copy   

•   Source: SciCrunch Registry

http://webclu.bio.wzw.tum.de/profcom/

Profiling of Complex Functionality (ProfCom) is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of complex function. A complex function is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. Platform: Online tool

Proper citation: ProfCom - Profiling of complex functionality (RRID:SCR_005797) Copy   

•   Source: SciCrunch Registry

http://estbioinfo.stat.ub.es/apli/serbgov131/index.php

SerbGO is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one. Platform: Online tool

Proper citation: SerbGO (RRID:SCR_005798) Copy   

•   Source: SciCrunch Registry

http://www.snpedia.com/index.php/SNPedia

Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php

Proper citation: SNPedia (RRID:SCR_006125) Copy   

•   Source: SciCrunch Registry

http://cossmos.slu.edu/

Database to search through the nucleic acid structures from the Protein Data Bank and examine structural motifs, including (a)symmetric internal loops, bulge loops, and hairpin loops. They have compiled over 2,000 three-dimensional structures, which can now be searched using different parameters, including PDB information, experimental technique, sequence, and motif type. RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop''''s structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is updated weekly.

Proper citation: RNA CoSSMos (RRID:SCR_006120) Copy   

•   Source: SciCrunch Registry

http://gopubmed.org/web/gopubmed/

A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool

Proper citation: GoPubMed (RRID:SCR_005823) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/expressionprofiler/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.

Proper citation: Expression Profiler (RRID:SCR_005821) Copy   

•   Source: SciCrunch Registry