ProgrammableWeb API Category: Genetics

Recent Genetics News/View all
Most Popular Genetics APIs (10) /View all
All Genetics APIs (81)/View all
Name Description Category Date
GA4GH Genomics
The Genomic Data Working Group is a coalition assembled to create interoperability standards for storing and sharing genomic data. The GA4GH Genomics API offers Interoperability for exchanging... Genetics 08.01.2014
iGEM Registry
iGEM, the International Genetically Engineered Machine competition, is an international undergraduate Synthetic Biology competition. Student teams are given a kit of standard biological parts and... Science 02.07.2014
Mammalian Adult Neurogenesis Gene Ontology
The Mammalian Neurogenesis Gene Ontology (MANGO) is a searchable database describing the key stages in the development of adult hippocampal neural stem cells. MANGO is exposed to developers through... Science 01.21.2014
MG-RAST
MG-RAST is a metagenomics analysis server, which is designed to provide quantitative information on microbial populations based on genetic sequence data. The server contains over 100,000 data set,... Science 12.17.2013
GenoLogics
GenoLogics provides the Clarity LIMS (Laboratory Information Management System), which is designed to help genomics and mass spec laboratories collect data, track samples and workflows, integrate... Science 11.14.2013
Mashups (1)/View all
Name Description Category Date
spatialepidemiology
Providing mapping tools for the global epidemiology of infectious disease. Datasets are available to interrogate geographically allowing researchers to investigate the epidemiology, evolution and... Medical 02.06.2008
Developers (1)

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Name Description Category Date
GA4GH Genomics
The Genomic Data Working Group is a coalition assembled to create interoperability standards for storing and sharing genomic data. The GA4GH Genomics API offers Interoperability for exchanging... Genetics 08.01.2014
iGEM Registry
iGEM, the International Genetically Engineered Machine competition, is an international undergraduate Synthetic Biology competition. Student teams are given a kit of standard biological parts and... Science 02.07.2014
Mammalian Adult Neurogenesis Gene Ontology
The Mammalian Neurogenesis Gene Ontology (MANGO) is a searchable database describing the key stages in the development of adult hippocampal neural stem cells. MANGO is exposed to developers through... Science 01.21.2014
MG-RAST
MG-RAST is a metagenomics analysis server, which is designed to provide quantitative information on microbial populations based on genetic sequence data. The server contains over 100,000 data set,... Science 12.17.2013
GenoLogics
GenoLogics provides the Clarity LIMS (Laboratory Information Management System), which is designed to help genomics and mass spec laboratories collect data, track samples and workflows, integrate... Science 11.14.2013
AILUN
AILUN is a service that allows users to search for and re-annotate data from GEO, a public repository of gene expressions and proteomics data. AILUN also allows users to compare genetic and... Science 09.16.2013
GenomeNet Tools
GenomeNet provides a network of databases and computational services related to research on genomics and other biomedical sciences. The GenomeNet Tools API provides chemical analysis tools for... Science 09.16.2013
DGIdb
The Drug Gene Interaction Database (DGIdb) is a database of known and potential drug-gene interactions. The web interface allows users to search for drug-gene interactions by gene, search for genes... Medical 08.19.2013
TMHMM
The service provides statistical predictions of membrane protein structures based on a hidden Markov model. It accepts amino acid sequences as input and generates expected transmembrane helices... Science 02.21.2013
SignalP/SignalP4
The service provides predictions of genetic structures based on neural network algorithms and Markov statistical models. It analyzes data about the frequency of amino acid sequences for various... Science 02.21.2013
GeneProf
The service provides data to support genetic research. Its data analysis functions help with processing of genetic sequences in RNA-seq and ChIP-seq formats, and a database of previously processed... Science 02.11.2013
GeneCoDis2
The service provides analysis of genetic sequence data to identify those associated with biological features, known as annotations, that frequently appear together. It then ranks these sets of genes... Science 02.04.2013
BioMortar
The service provides a modeling environment for assembling and combining BioBricks, which are standardized packages of genetic patterns encoded to generate discrete biological functions. In... Science 01.21.2013
PcProf predict physico-chemical profiles of proteins
The service provides a profile of a submitted protein sequence, describing its characteristics in relation to a list of properties established for known structures. Characteristics described include... Science 01.14.2013
COILS predict protein coiled-coil regions
The service provides predictions of coiled-coil regions within a protein structure through application of an algorithm from Lupas et al. It assesses the probability that some part of a protein... Science 01.14.2013
PREDATOR protein secondary structure prediction
The service predicts secondary protein structures by analyzing amino acid sequences submitted and detecting hydrogen-bonded residues within those structures. Potential for hydrogen bonds is... Science 01.14.2013
GOR protein secondary structure prediction
This collection of three services -- GORI, GORIII, and GORIV -- provide predictions of secondary protein sequences using methods based on the information theory of Garnier, Osguthorpe, and Robson. It... Science 01.14.2013
DSC protein secondary structure prediction
The service provides predictions of secondary protein structures by assigning a test sequence to one class of such structures based on statistical measures of probability. This method decomposes the... Science 01.14.2013
SSearch protein similarity search
The service compares a submitted protein sequence against a reference database with analysis of similarities to known sequences. The output helps to identify a sequence and establish its genetic... Science 01.14.2013
FastA protein similarity search
The service compares a protein sequence submitted with a request against a database of protein structures. It reports matches with known protein sequences, indicating genetic relationships between... Science 01.14.2013
MultAlin
The service detects multiple alignments of elements within protein sequences submitted. Comparison of sequences detected in multiple sources can reveal similarities that indicate shared genetic... Science 01.14.2013
SIMPA96
The service provides predictions of secondary protein and nucleic acid sequences implied by the presence of known primary sequences. Its analysis is based on the nearest neighbor methodology, which... Science 01.14.2013
Pseudoviewer
The service provides tools for creating visual representations of genetic structures involving RNA. It converts experimental data to depict secondary structures and pseudoknot structures. By... Science 01.14.2013
ALTER Reflective
The service provides conversion of DNA and protein alignment sequences from biological research to express the same information in alternative notation and as input for a different analytical... Science 12.26.2012
JasparDB
The service provides access to a database of factor-binding profiles depicting genetic makeups and structures typical of species. It provides biological researchers with lookup access to matrices... Science 12.05.2012
Retrotector
The service from the University of Uppsala in Sweden provides analysis of DNA sequence data to generate a viewable representation of genetic links represented. A Java-based viewer program is... Science 12.04.2012
Madeline
The service provides analysis and formatting of data reflecting human genetic background for use in studies of genetic linkage and pedigree. It converts data about genetic markers for an individual... Science 11.26.2012
Ensembl
Ensembl is a joint project between EMBL - EBI and the Wellcome Trust Sanger Institute. The project produces genome databases for vertebrates and other eukaryotic species including mice, humans,... Science 11.20.2012
Illumina BaseSpace
BaseSpace by Illumina is a application for genetic data and analysis and genomics cloud computing. The BaseSpace API allows developers to access and integrate the functionality of BaseSpace with... Science 11.04.2012
OMIM
OMIM (Online Mendelian Inheritance in Man) is a comprehensive, freely available, and authoritative compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM... Science 10.16.2012
CIPF RENATO
The service provides a RESTful interface to RENATO (REgulatory Network Analysis TOol) which provides network-based analysis to identify regulatory elements common to a list of genes. It is intended... Science 10.16.2012
WebScipio
The service defines the gene structure implied by a protein sequence within a particular genome. It aides in research projects to define gene sequencing by analyzing a protein sequence and... Science 10.03.2012
23andMe
23andMe is a personal genetics service. 23andMe offers individual genome and DNA testing and information. The 23andMe API allows developers to access and integrate the data from 23andMe with other... Science 09.14.2012
openSNP
openSNP allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results, find the latest primary... Science 08.15.2012
Genome Maps
Genome Maps is a genome browser service that allows real-time navigation along chromosomes and karyotypes. Genomic data in different standard formats (GFF, BED, VCF) can be easily imported and... Science 06.27.2012
BioDB Hyperlink Management System
The service maintains and automatically updates a database of hyperlinks across major biology and life sciences databases. It defines stable identifiers linking to data IDs in major databases for... Science 05.29.2012
cBio Cancer Genomics Data Server (CGDS)
The service provides direct access by applications to genetic and genomic data stored by the Memorial Sloan-Kettering Cancer Center. Applications can retrieve information about cancer studies and... Science 04.10.2012
Visual Omics aGEM
aGEM (anatomic Gene Expression Mapping) is designed to integrate phenotypic information from spatial and temporal distributions of expressed genes. It provides easy access to information on gene... Science 04.01.2012
Regulatory Sequence Analysis Tools
Regulatory Sequence Analysis Tools (RSAT) offers a series of applications dedicated to the detection of regulatory signals in non-coding DNA sequences. The only input required is a list of genes of... Science 04.01.2012
GenomeMatrix
GenomeMatrix performs parallel genome analyses and connects multi-species functional information with a collection of manually curated experimental data. It is capable of displaying multi-species... Science 03.31.2012
G-language GAE
G-language Genome Analysis Environment (G-language GAE) is a set of Perl libraries for genome sequence analysis. It includes more than 100 original analysis programs and tends to focus on bacterial... Science 03.22.2012
Mutalyzer
Mutalyzer provides a suite of services that check variant sequence nomenclature according to the guidelines of the Human Genome Variation Society. These services allow users to assess the correctness... Science 03.21.2012
AnnotQTL
AnnotQTL is a tool designed to gather the functional annotations of genes for specific chromosomal regions. It provides the locations of genes in a specific region using NCBI and Ensembl data. Then,... Science 03.21.2012
MyGene.Info
MyGene.Info provides a simple REST-based API to retrieve gene annotation data. Such data is currently available for seven species: human, mouse, rat, fruitfly, nematode, zebrafish, thale-cress, and... Science 03.21.2012
FlyMine
The service aggregates genetic data about fly organisms commonly used in biological research: Drosophila, Anopheles and C. elegans. It documents the genomes and protein data for these animals,... Science 03.19.2012
e-Fungi
e-Fungi provides a database that integrates data on multiple fungal genomes, including 23 fungi and 2 oomycetes. It does so in such a way as to facilitate the systematic comparative study of those... Science 03.04.2012
ncRNA fRNAdb
The service provides search access to a database of functional RNA sequences. It is part of a web portal of bioinformatics tools supporting genetic research specific to functional RNA, it is a... Science 03.02.2012
Mouse Resource Browser
The Mouse Resource Browser (MRB) provides a dynamic and interactive view of 222 mouse-related bioinformatics resources from around the world. The SOAP-based MRB API can be used to retrieve data such... Science 02.29.2012
Genomic Name Server
Genomic Name Server (GeNS) provides unified access to data residing at different sources, under different schemas, and in different formats. Currently, GeNS is importing data from four major... Science 02.29.2012
FlyBase
FlyBase is an online database of Drosophila (fruit fly) genes and genomes. The FlyBase API allows users to retrieve Chado XML data for FlyBase objects using either the primary FlyBase ID or current... Science 02.28.2012
Duplicated Genes Database
The Duplicated Genes Database (DGD) provides a list of co-located and duplicated genes. These genes may be either tandem repeats or members of the same multigene family. Lists of duplicated genes can... Science 02.21.2012
The SEED
The SEED is a database for annotated genomic information. It was started in 2003 by the Fellowship for Interpretation of Genomes. Other institutions, such as Argonne National Laboratory and the... Science 02.21.2012
miRMaid
miRMaid provides programmatic access to data in miRBase, a major database for microRNA (abbreviated miRNA) information. miRNA is a short ribonucleic acid (RNA) molecule found in eukaryotic cells. The... Science 02.21.2012
Center for Biological Sequence Analysis
The Center for Biological Sequence Analysis offers a collection of SOAP-based APIs for working with nucleotide sequences, amino acid sequences, and small molecules. The nucleotide sequence APIs... Science 02.21.2012
EBI Lalign
Lalign is a program for the local pairwise alignment of DNA and protein sequences. It finds internal duplications by calculating non-intersecting local alignments in the two sequences input by the... Science 02.13.2012
EMBOSS Water
EMBOSS Water is a program for performing local pairwise sequence alignments on DNA or protein sequences. Using the Smith-Waterman local alignment algorithm (modified for speed enhancements), this... Science 02.13.2012
EMBOSS Stretcher
EMBOSS Stretcher is a program for performing global pairwise sequence alignments on DNA or protein sequences. Using the Myers and Miller global alignment algorithm, EMBOSS Stretcher calculates an... Science 02.13.2012
EMBOSS Needle
EMBOSS Needle is a program for performing global pairwise sequence alignments on DNA or protein sequences. Using the Needleman-Wunsch global alignment algorithm, this program takes two protein or... Science 02.13.2012
EMBOSS Matcher
EMBOSS Matcher is a program for performing local pairwise sequence alignments on DNA or protein sequences. It employs the Waterman-Eggert local alignment algorithm to identify local similarities in... Science 02.13.2012
EBI ClustalW2
ClustalW2 is a program for the global multiple alignment of biological sequences. It can align anywhere from 3 to 500 DNA or protein sequences. One notable feature of this alignment program is that... Science 02.12.2012
EBI T-Coffee
T-Coffee (Tree-based Consistency Objective Function For alignmEnt Evaluation) is a program that performs multiple sequence alignments on DNA, RNA, and protein sequences. The program's most... Science 02.07.2012
EBI PRANK
PRANK is a probabilistic multiple alignment program for DNA, codon, and amino-acid sequences. It also allows users to define a potential structure for sequences to be aligned to and predicts the... Science 02.07.2012
EBI MUSCLE
MUSCLE (MUltiple Sequence Comparison by Log-Expectation) is a tool for the alignment of multiple nucleotide or amino acid sequences. Multiple sequence alignments are a crucial part of processing... Science 02.07.2012
EBI MAFFT
MAFFT (Multiple Alignment using Fast Fourier Transform) is a multiple sequence alignment program for protein and nucleic acid sequences. It offers a range of multiple alignment methods that make it... Science 02.07.2012
EBI Kalign
Kalign was developed to improve the speed and accuracy of multiple sequence alignments, which are a fundamental part of analyzing biological data. It uses the fast and accurate Wu-Manber string-... Science 02.07.2012
EBI Phobius
Phobius is a tool that uses the amino acid sequence of a protein to predict transmembrane topology (which regions of the polypeptide chain span the lipid bilayer) and to identify potential signal... Science 02.07.2012
EMBOSS Transeq
The EMBOSS Transeq API translates nucleic acid sequences into their corresponding peptide sequences. It can translate the three forward and three reverse reading frames found in DNA, and output... Science 02.03.2012
EMBOSS Sixpack
The EMBOSS Sixpack API reads a DNA sequence that's been input by the user and then outputs the three forward and (optionally) three reverse frame translations in a visual manner. The API is... Science 02.03.2012
EMBOSS Backtranseq
The EMBOSS Backtranseq API reads a protein sequence input by the user and then outputs the nucleic acid sequence that is most likely to have produced it. To determine the nucleic acid sequence, the... Science 02.03.2012
EMBOSS Backtranambig
The EMBOSS Backtranambig API reads a protein sequence input by the user and then writes the nucleic acid sequence it could have come from. To do so, it uses nucleotide ambiguity codes that represent... Science 02.03.2012
OligoSelection
The OligoSelection API was created to help minimize the cost of DNA microarray experiments, which are used to determine the presence or absence of specific biological units in DNA. The API minimizes... Science 02.03.2012
HUSAR Bioinformatics Lab
The HUSAR Bioinformatics Lab at DKFZ provides a large number of freely available APIs. Many of these are useful in aligning DNA, RNA, or protein sequences. Alignments can be pairwise or multiple,... Science 02.03.2012
DKFZ SoapDB
The SoapDB API provides SOAP-based access to the more than 200 genetics and protein sequence databases. The user can filter results by field and select a format or view for returned data. Access to... Science 02.03.2012
Phylogenetic Footprinting
"Phylogenetic Footprinting" is an approach for identifying regulatory regions of genes by comparing orthologous non-coding sequences. The Phylogenetic Footprinting API created and managed... Science 02.03.2012
Roci
Roci (Reconstruction Of Conserved Intervals) is a tool for reconstructing the ancestral gene orders of phylogenetic trees. Given the branching pattern of a phylogenetic tree and the gene orders of... Science 01.26.2012
Divide-and-Conquer Multiple Sequence Alignment
Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing fast, high quality, simultaneous multiple alignments of amino acid, RNA, or DNA sequences. The program is based on an... Science 01.26.2012
Reputer
The Reputer API helps users discover and visualize repeats in whole genomes or chromosomes. Repeat types that can be searched for include forward(direct) matches, reverse matches, complement matches... Science 01.26.2012
RNAforester
RNAforester is a tool for comparing RNA secondary structures. It supports the computation of pairwise structures and the multiple alignment of structures. RNAforester is available as a web console or... Science 01.26.2012
RNAfold
RNAfold is an interface for RNA folding and sequence design. It can be used to calculate secondary structures of RNA sequences. RNAfold is available as a web console or as a SOAP API. Science 01.26.2012
KnotInFrame
KnotInFrame predicts frameshift sites in DNA and RNA sequences with a simple pseudoknot as secondary structure. The prediction is based on a comparison of minimal free energy structures. KnotInFrame... Science 01.26.2012
RNAshapes
Given an RNA sequence, RNAshapes can help determine its probable shape. RNAshapes computes a small set of representative structures of different shapes as well as accumulated shape probabilities. It... Science 01.26.2012
Name Description Category Date
spatialepidemiology
Providing mapping tools for the global epidemiology of infectious disease. Datasets are available to interrogate geographically allowing researchers to investigate the epidemiology, evolution and... Medical 02.06.2008

No Framework/Librarys

Name Description Category Date
Ruby Class for Ensembl API
Provides a Ruby class for EBI's Ensembl database which contains genetics and genomics mapping data (at http://www.ensembl.org). Genetics 11.10.2008