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https://www.schrodinger.com/protein-preparation-wizard

Software tool for correcting common structural problems and creating reliable, all atom protein models.

Proper citation: Protein preparation Wizard (RRID:SCR_016749) Copy   

•   Source: SciCrunch Registry
  

https://www.openepi.com/Menu/OE_Menu.htm

Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection.

Proper citation: OpenEpi (RRID:SCR_021913) Copy   

•   Source: SciCrunch Registry
  

http://scholar.google.com/

Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources

Proper citation: Google Scholar (RRID:SCR_008878) Copy   

•   Source: SciCrunch Registry
  

http://tcoffee.crg.cat/apps/tcoffee/do:regular

A multiple sequence alignment server which can align Protein, DNA and RNA sequences.

Proper citation: T-Coffee (RRID:SCR_011818) Copy   

•   Source: SciCrunch Registry
  

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry
  

http://genevenn.sourceforge.net/

A web application creating Venn diagrams from two or three gene lists.

Proper citation: GeneVenn (RRID:SCR_012117) Copy   

•   Source: SciCrunch Registry
  

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Tool to search translated nucleotide databases using a protein query.

Proper citation: TBLASTN (RRID:SCR_011822) Copy   

•   Source: SciCrunch Registry
  

http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains).

Proper citation: FGENESH (RRID:SCR_011928) Copy   

•   Source: SciCrunch Registry
  

http://gpcr.biocomp.unibo.it/bacello/

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry
  

http://Mar2008.archive.ensembl.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website).

Proper citation: Ensembl Genome Browser (RRID:SCR_013367) Copy   

•   Source: SciCrunch Registry
  

https://www.webofscience.com/wos/woscc/advanced-search

Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database.

Proper citation: Web of Science (RRID:SCR_022706) Copy   

•   Source: SciCrunch Registry
  

http://www-stat.stanford.edu/~tibs/SAM/

Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments.

Proper citation: SAM (RRID:SCR_010951) Copy   

•   Source: SciCrunch Registry
  

http://bioinformatics.vub.ac.be/databases/databases.html

Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs

Proper citation: SABmark (RRID:SCR_011817) Copy   

•   Source: SciCrunch Registry
  

http://www.stata.com

Software package for statistical analysis and presentation of graphics. Statistical software for data science.

Proper citation: Stata (RRID:SCR_012763) Copy   

•   Source: SciCrunch Registry
  

https://www.statease.com/software/design-expert/

Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs.

Proper citation: Design-Expert (RRID:SCR_022671) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.inria.fr/Phylophile/Treerecs

Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree.

Proper citation: Treerecs (RRID:SCR_024497) Copy   

•   Source: SciCrunch Registry
  

https://www.evalue-calculator.com/evalue/

Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences.

Proper citation: Evalue (RRID:SCR_024506) Copy   

•   Source: SciCrunch Registry
  

http://www.biogazelle.com/qbaseplus

Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.

Proper citation: qBasePLUS (RRID:SCR_003370) Copy   

•   Source: SciCrunch Registry
  

Ratings or validation data are available for this resource

http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) Copy   

•   Source: SciCrunch Registry
  

http://www.sas.com

Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS.

Proper citation: Statistical Analysis System (RRID:SCR_008567) Copy   

•   Source: SciCrunch Registry