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http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/

WebProAnalyst provides web-accessible analysis for scanning the quantitative structure-activity relationships in protein families. It searches for a sequence region, whose substitutions are correlated with variations in the activities of a homologous protein set, the so-called activity modulating sites. WebProAnalyst allows users to search for the key physicochemical characteristics of the sites that affect the changes in protein activities. It enables the building of multiple linear regression and neural networks models that relate these characteristics to protein activities. WebProAnalyst implements multiple linear regression analysis, back propagation neural networks and the Structure-Activity Correlation/Determination Coefficient (SACC/SADC). A back propagation neural network is implemented as a two-layered network, one layer as input, the other as output (Rumelhart et al, 1986). WebProAnalyst uses alignment of amino acid sequences and data on protein activity (pK, Km, ED50, among others). The input data are the numerical values for the physicochemical characteristics of a site in the multiple alignment given by a slide window. The output data are the predicted activity values. The current version of WebProAnalyst handles a single activity for a single protein. The SACC/SADC may be defined as an estimate of the strongest multiple correlation between the physicochemical characteristics of a site in a multiple alignment and protein activities. The SACC/SADC coefficient makes possible the calculation of the possible highest correlation achievable for the quantitative relationship between the physicochemical properties of sites and protein activities. The SACC/SADC is a convenient means for an arrangement of positions by their functional significance. WebProAnalyst outputs a list of multiple alignment positions, the respective correlation values, also regression analysis parameters for the relationships between the amino acid physicochemical characteristics at these positions and the protein activity values.

Proper citation: Webproanalyst (RRID:SCR_008348) 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://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

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

https://github.com/DerrickWood/kraken2

Software tool as second version of Kraken taxonomic sequence classification system.

Proper citation: kraken2 (RRID:SCR_026838) Copy   

•   Source: SciCrunch Registry

http://www.brenda-enzymes.org/

Database for functional enzyme and ligand-related information maintained as part of the German ELIXIR Node. Provides advanced query systems, evaluation tools, and various visualization options for the detailed assessment of enzyme properties. Enzyme data in BRENDA are classified according to the Enzyme Commission (EC) nomenclature of IUBMB.

Proper citation: BRENDA (RRID:SCR_002997) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/polyphred/

Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.

Proper citation: PolyPhred (RRID:SCR_002337) 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.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://sfld.rbvi.ucsf.edu/

A database of hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. The SFLD classifies evolutionarily related enzymes according to shared chemical functions and maps these shared functions to conserved active site features. The classification is hierarchical, where broader levels encompass more distantly related proteins with fewer shared features. It thus serves as the analysis and archive site for superfamilies targeted by the Enzyme Function Initiative, and is developed by the Babbitt Laboratory in collaboration with the UCSF Resource for Biocomputing, Visualization, and Informatics. The resource also provides a collection of tools and data for investigating sequence-structure-function relationships and hypothesizing function.

Proper citation: Structure-function linkage database (RRID:SCR_001375) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/ProViDE/

A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProViDE (RRID:SCR_004709) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/DiScRIBinATE/

Software for accurate taxonomic classification of metagenomic sequences using a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr protein database using BLASTx search. The generated blastx output is then taken as the input by the DiScRIBinATE program.

Proper citation: DiScRIBinATE (RRID:SCR_004862) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://khavarilab.stanford.edu/resources.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.

Proper citation: RINS (RRID:SCR_003652) 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

https://github.com/benedictpaten/pecan

A Java consistency based multiple sequence alignment software program.

Proper citation: Pecan (RRID:SCR_001909) Copy   

•   Source: SciCrunch Registry