GE Healthcare (tool)

RRID:SCR_000004

A commercial antibody supplier and provider of various services.

ATCC (tool)

RRID:SCR_001672

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

Thermo Fisher Scientific (tool)

RRID:SCR_008452

Commercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.

Covance (tool)

RRID:SCR_001224

A contract research organization providing drug development and animal testing services. Under the name Covance Research Products Inc., based in Denver, Pennsylvania, the company also deals in the import, breeding and sale of laboratory animals. It breeds dogs, rabbits, guinea pigs, non-human primates, and pigs, and runs the largest non-human primate laboratory in Germany. (Wikipedia)

SMART (tool)

RRID:SCR_005026

Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.

NIH AIDS Reagent Program (tool)

RRID:SCR_023191

NIH HIV Reagent Program has been managed under contract by American Type Culture Collection (ATCC) since 2020. ATCC shall maintain the NIH HIV Reagent Program through identification, acquisition, production, receipt, storage, maintenance, distribution and disposal of biological and chemical research organisms and materials for HIV and other infectious diseases for use in basic and translational research.

Monoclonal ANTI-FLAG® M2 antibody produced in mouse (antibody)

RRID:AB_262044

This monoclonal targets FLAG

HSP 90 (4F10) (antibody)

RRID:AB_2121191

This monoclonal targets HSP 90 (4F10)

MCT1 (H-1) (antibody)

RRID:AB_10841766

This monoclonal targets MCT1 (H-1)

Influenza hemagglutinin epitope (YPYDVPDYA) (antibody)

RRID:AB_2314672

This unknown targets

Anti-HA EPITOPE TAG (RABBIT) Antibody - 600-401-384 (antibody)

RRID:AB_217929

This polyclonal targets HA EPITOPE TAG Antibody

PAML (software resource)

RRID:SCR_014932

Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree.

CV-1 (cell line)

RRID:CVCL_0229

Cell line CV-1 is a Finite cell line with a species of origin Chlorocebus aethiops

K-562 (cell line)

RRID:CVCL_0004

Cell line K-562 is a Cancer cell line with a species of origin Homo sapiens (Human)

UMNSAH/DF-1 (cell line)

RRID:CVCL_0570

Cell line UMNSAH/DF-1 is a Spontaneously immortalized cell line with a species of origin Gallus gallus

R187 (cell line)

RRID:CVCL_9230

CHO-K1 (cell line)

RRID:CVCL_0214

Cell line CHO-K1 is a Spontaneously immortalized cell line with a species of origin Cricetulus griseus (Chinese hamster)

MDCK (cell line)

RRID:CVCL_0422

Cell line MDCK is a Spontaneously immortalized cell line with a species of origin Canis lupus familiaris

CRFK (cell line)

RRID:CVCL_2426

Cell line CRFK is a Spontaneously immortalized cell line with a species of origin Felis catus (Cat)

MRC-5 (cell line)

RRID:CVCL_0440

Cell line MRC-5 is a Finite cell line with a species of origin Homo sapiens

Rat2 (cell line)

RRID:CVCL_0513

Cell line Rat2 is a Spontaneously immortalized cell line with a species of origin Rattus norvegicus

M. dunni (Clone III8C) (cell line)

RRID:CVCL_9125

Cell line M. dunni (Clone III8C) is a Spontaneously immortalized cell line with a species of origin Mus terricolor

FRhK-4 (cell line)

RRID:CVCL_4522

Cell line FRhK-4 is a Spontaneously immortalized cell line with a species of origin Macaca mulatta (Rhesus macaque)

HT-1080 (cell line)

RRID:CVCL_0317

Cell line HT-1080 is a Cancer cell line with a species of origin Homo sapiens (Human)

HEK293T (cell line)

RRID:CVCL_0063

Cell line HEK293T is a Transformed cell line with a species of origin Homo sapiens (Human)

Huh-7.5 (cell line)

RRID:CVCL_7927

Cell line Huh-7.5 is a Cancer cell line with a species of origin Homo sapiens (Human)

NIH 3T3 (cell line)

RRID:CVCL_0594

Cell line NIH 3T3 is a Spontaneously immortalized cell line with a species of origin Mus musculus

MT-2 (cell line)

RRID:CVCL_2631

Cell line MT-2 is a Transformed cell line with a species of origin Homo sapiens

ProP Server (web application)

RRID:SCR_014936

Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.

TMHMM Server (web application)

RRID:SCR_014935

Web application for the prediction of transmembrane helices in proteins using Hidden Markov Models. FASTA formatted sequences can be uploaded via file or copy-paste, and output can be formatted as extensive with graphics, extensive without graphics, or one line per protein. Submissions are limited to 10,000 sequences and 4,000,000 amino acids - each sequence is limited to no more than 8,000 amino acids.

Seq-Gen (software resource)

RRID:SCR_014934

Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.

R Project for Statistical Computing (software resource)

RRID:SCR_001905

Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

UCSC Genome Browser (data or information resource)

RRID:SCR_005780

Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.

Hypermut (software resource)

RRID:SCR_014933

Web application for the analysis and detection of APOBEC-induced hypermutations. The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence.

PAUP (software resource)

RRID:SCR_014931

Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis.

FigTree (data processing software)

RRID:SCR_008515

A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.

RAxML (software resource)

RRID:SCR_006086

Software program for phylogenetic analyses of large datasets under maximum likelihood.

MUSCLE (software resource)

RRID:SCR_011812

Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.

RefSeq (data or information resource)

RRID:SCR_003496

Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.

BLASTX (data analysis service)

RRID:SCR_001653

Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.

BLASTN (data analysis service)

RRID:SCR_001598

Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.

TBLASTN (service resource)

RRID:SCR_011822

Tool to search translated nucleotide databases using a protein query.

PAML (software resource)

RRID:SCR_014932

Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree.