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ProteomicsEvaluating sequence alignment for metaproteomics applications
This dataset was utilized to assess the performance of a novel de novo metaproteomics pipeline, which performs sequence alignment of de novo sequences from complete metaproteomics experiments. Traditionally, metaproteomics data annotation relies on database searching that requires sample-specific da...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-10-10 | PXD050548 | Pride
Microbial proteomics Sequence alignment De novo sequencing Metaproteomics 
TranscriptomicsRNA-seq read alignment evaluation
To assess the performance of read mapping software for RNA-seq, 26 spliced alignment protocols based on 11 programs and pipelines (BAGET, GEM, GSNAP, GSTRUCT, MapSplice, PALMapper, PASS, ReadsMap, SMALT, STAR and TopHat) were applied to four human and mouse transcriptome data sets.
ORGANISM(S): Homo sapiens 
2013-07-15 | E-MTAB-1728 | biostudies-arrayexpress
TranscriptomicsRNA-seq alignment to individualized genomes
The source of most errors in RNA sequencing (RNA-seq) read alignment is in the repetitive structure of the genome and not with the alignment algorithm. Genetic variation away from the reference sequence exacerbates this problem causing reads to be assigned to the wrong location. We developed a metho...
ORGANISM(S): Mus musculus 
2014-06-10 | E-GEOD-45684 | biostudies-arrayexpress
TranscriptomicsU87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades. In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30x genomic s...
ORGANISM(S): Homo sapiens 
2010-01-24 | E-GEOD-19986 | biostudies-arrayexpress
TranscriptomicsComparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM).
A critical task in high throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency ...
ORGANISM(S): Mus musculus 
2011-08-03 | E-GEOD-26248 | biostudies-arrayexpress
UnknownSeedability: optimizing alignment parameters for sensitive sequence comparison.
Not available
S-EPMC10444664 | biostudies-literature
UnknownAn enhanced RNA alignment benchmark for sequence alignment programs.
Not available
S-EPMC1635699 | biostudies-literature
UnknownGapped sequence alignment using artificial neural networks: application to the MHC class I system.
Not available
S-EPMC6402319 | biostudies-literature
UnknownContact-based sequence alignment.
Not available
S-EPMC419454 | biostudies-literature
UnknownMaxAlign: maximizing usable data in an alignment.
Not available
S-EPMC2000915 | biostudies-literature
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