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ALEXA-Seq | Alternative expression analysis by RNA sequencing

Analyzes parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. ALEXA-Seq comprises several functions: (1) creation of a database of expression and alternative expression sequence ‘features’, (2) mapping of short paired-end sequence reads to these features, (3) identification of features that are expressed above background noise while taking into account locus-by-locus noise, or (4) identification of features that are differentially expressed in samples.

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ALEXA-Seq forum

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ALEXA-Seq classification

ALEXA-Seq specifications

Unique identifier:
OMICS_01328
Interface:
Command line interface
Input data:
Some EnsEMBL gene models or mRNA and EST alignments.
Computer skills:
Advanced
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Stability:
Stable

ALEXA-Seq distribution

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No versioning.

Credits

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Publications

Institution(s)

Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Department of Medicine, University of British Columbia, Vancouver, BC, Canada

Funding source(s)

Supported by the University of British Columbia, the Michael Smith Foundation for Health Research, the Natural Sciences and Engineering Research Council, Genome British Columbia, the Terry Fox Foundation, the Canadian Institutes of Health Research, the National Cancer Institute of Canada and the British Columbia Cancer Foundation.

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