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UnknownMaking whole genome multiple alignments usable for biologists.

Summary

Here we describe a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface.

Availability an...

S-EPMC3157923 | biostudies-literature
UnknownReproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses.

Background

Significant progress has been made in advancing and standardizing tools for human genomic and biomedical research. Yet, the field of next-generation sequencing (NGS) analysis for microorganisms (including multiple pathogens) remains fragmented, lacks accessible and reusable tools,...
S-EPMC8178898 | biostudies-literature
UnknownMaternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.
The manifestation of mitochondrial DNA (mtDNA) diseases depends on the frequency of heteroplasmy (the presence of several alleles in an individual), yet its transmission across generations cannot be readily predicted owing to a lack of data on the size of the mtDNA bottleneck during oogenesis. For d...
S-EPMC4217420 | biostudies-literature
GenomicsHistone Modifications by ChIP-seq from ENCODE/PSU
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Ross Hardison mailto:rch8@psu.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). Rationale for the Mou...
ORGANISM(S): Mus musculus 
2012-06-11 | E-GEOD-36028 | biostudies-arrayexpress
GenomicsTranscription Factor Binding Sites by ChIP-seq from ENCODE/PSU
Rationale for the Mouse ENCODE project Our knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approach...
ORGANISM(S): Mus musculus 
2012-04-29 | E-GEOD-36029 | biostudies-arrayexpress
GenomicsDNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Ross Hardison mailto:rch8@psu.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). Rationale for the Mous...
ORGANISM(S): Mus musculus 
2012-09-13 | E-GEOD-40848 | biostudies-arrayexpress
UnknownScalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.
Not available
S-EPMC11462542 | biostudies-literature
GenomicsHistone Modifications by ChIP-seq from ENCODE/Caltech
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Barbara Wold mailto:woldb@caltech.edu, Georgi K. Marinov mailto:georgi@caltech.edu, Diane Trout mailto:diane@caltech.edu). If you have questions about the Genome Browser track associa...
ORGANISM(S): Mus musculus 
2012-04-19 | E-GEOD-36023 | biostudies-arrayexpress
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