Embedded Files
Ensembl Biomart
Ensembl Biomart
"BioMart is an easy-to-use web-based tool that allows extraction of data without any programming knowledge or understanding of the underlying database structure. You can navigate through the BioMart web interface using the left panel. Filters and attributes can be selected in the right panel. A summary of your choices is also displayed in the left panel."
"BioMart is an easy-to-use web-based tool that allows extraction of data without any programming knowledge or understanding of the underlying database structure. You can navigate through the BioMart web interface using the left panel. Filters and attributes can be selected in the right panel. A summary of your choices is also displayed in the left panel."
wANNOVAR
wANNOVAR
"ANNOVAR is a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data. wANNOVAR provides easy and intuitive web-based access to the most popular functionalities of the ANNOVAR software"
"ANNOVAR is a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data. wANNOVAR provides easy and intuitive web-based access to the most popular functionalities of the ANNOVAR software"
ToppGene Suite
ToppGene Suite
"Toppgene: functional annotations-based candidate gene prioritization. ToppGene works by generating a representative profile of the training genes using as many as 14 features and identifies over-representative terms from the training genes." Link
"Toppgene: functional annotations-based candidate gene prioritization. ToppGene works by generating a representative profile of the training genes using as many as 14 features and identifies over-representative terms from the training genes." Link
Galaxy
Galaxy
"Rapid growth in FAIR data, and an expanding range of open source analysis software packages, offer rich research opportunities in data intensive fields such as genome science. Galaxy offers powerful and practical solutions for analyzing this data by providing access to extensive hardware, tools, and data that can be adopted with relatively minimal training. The open source software allows scientists to efficiently manage their own data, and to share transparent, reproducible analyses. More than 8000 popular analysis software packages have been integrated with Galaxy and their use is supported via numerous topic-based training resources. The growing breadth of tools available in Galaxy enables diverse types of analysis and because all data manipulations are performed via tools (as opposed to ad-hoc scripts or manual editing), reproducibility is ensured. " Link
"Rapid growth in FAIR data, and an expanding range of open source analysis software packages, offer rich research opportunities in data intensive fields such as genome science. Galaxy offers powerful and practical solutions for analyzing this data by providing access to extensive hardware, tools, and data that can be adopted with relatively minimal training. The open source software allows scientists to efficiently manage their own data, and to share transparent, reproducible analyses. More than 8000 popular analysis software packages have been integrated with Galaxy and their use is supported via numerous topic-based training resources. The growing breadth of tools available in Galaxy enables diverse types of analysis and because all data manipulations are performed via tools (as opposed to ad-hoc scripts or manual editing), reproducibility is ensured. " Link
ENCODE
ENCODE
"The human and mouse ENCODE Projects initiated programs to broaden and deepen their respective efforts to discover and annotate functional elements, and to systematize the production, curation, and dissemination of ENCODE data with the aim of broadly empowering the scientific community. ENCODE data have served as an enabling interface between the human genome sequence and its application to biomedical research because of both the range of biological and biochemical features encompassed by ENCODE assays and the breadth and depth with which these assays have been applied across cell and tissue contexts. " Link
"The human and mouse ENCODE Projects initiated programs to broaden and deepen their respective efforts to discover and annotate functional elements, and to systematize the production, curation, and dissemination of ENCODE data with the aim of broadly empowering the scientific community. ENCODE data have served as an enabling interface between the human genome sequence and its application to biomedical research because of both the range of biological and biochemical features encompassed by ENCODE assays and the breadth and depth with which these assays have been applied across cell and tissue contexts. " Link
NIH Roadmap Epigenomics Mapping Consortium
NIH Roadmap Epigenomics Mapping Consortium
"The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The project has generated high-quality, genome-wide maps of several key histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues."
"The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The project has generated high-quality, genome-wide maps of several key histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues."
BLAST
BLAST
"BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance."
"BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance."
BLAT
BLAT
"The program rapidly scans for relatively short matches (hits), and extends these into high-scoring pairs (HSPs). However, BLAT differs from BLAST in some significant ways. Where BLAST builds an index of the query sequence and then scans linearly through the database, BLAT builds an index of the database and then scans linearly through the query sequence." Link
"The program rapidly scans for relatively short matches (hits), and extends these into high-scoring pairs (HSPs). However, BLAT differs from BLAST in some significant ways. Where BLAST builds an index of the query sequence and then scans linearly through the database, BLAT builds an index of the database and then scans linearly through the query sequence." Link
mfold
mfold
Prediction of secondary structures of nucleic acids
Prediction of secondary structures of nucleic acids
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