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SalmonDB specifications

Information


Unique identifier OMICS_14320
Name SalmonDB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 87.1
Maintained Yes

Maintainer


  • person_outline Andrés Aravena

Publication for SalmonDB

SalmonDB citations

 (3)
library_books

The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs

2016
F1000Res
PMCID: 5007756
PMID: 27635217
DOI: 10.5256/f1000research.6869.r8970

[…] f the 36 bp reads yielded an excessive number of short contigs we chose to assess expression and genetic variation by mapping the reads to 59336 S. salar expressed sequence tag (EST) contigs from the SalmonDB [ , downloaded 22. March 2012] and the Arctic charr mitochondrial genome [ , NC_000861].To estimate expression, reads were aligned with RSEM version 1.1.18 with default parameters. RSEM distr […]

library_books

Differential expression of the aryl hydrocarbon receptor pathway associates with craniofacial polymorphism in sympatric Arctic charr

2015
PMCID: 4574265
PMID: 26388986
DOI: 10.1186/s13227-015-0022-6

[…] ow. To identify the conserved exon/intron boundaries of the candidate genes, the assembled charr contigs were aligned to the genomic sequences of salmon orthologs (retrieved from the salmon database, SalmonDB []) using the NCBI Spidey software (http://www.ncbi.nlm.nih.gov/spidey). Primers were designed using Primer Express 3.0 software (Applied Biosystems, Foster City, CA, USA) and checked for sel […]

library_books

Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr

2014
PMCID: 4240837
PMID: 25419450
DOI: 10.1186/2041-9139-5-40

[…] nd aligned charr contigs to the genomic sequences of zebrafish and salmon orthologs from the Ensembl database (http://useast.ensembl.org/Danio_rerio/Info/Index) and salmonids species database (http://salmondb.cmm.uchile.cl/) using the National Center for Biotechnology Information Spidey software (http://www.ncbi.nlm.nih.gov/spidey). Primers were designed using Primer Express 3.0 software (Applied […]

Citations

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SalmonDB institution(s)
Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation, University of Chile, Santiago, Chile; Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Chile; ICBM Human Genetics Program, Faculty of Medicine, University of Chile, Santiago, Chile; Laboratorio de Bioinformatica y Expresion Génica, INTA, University of Chile, Santiago, Chile
SalmonDB funding source(s)
The work was supported by CORFO-INNOVA (grant 07CN13PBT-41); Fondecyt (1110427) and Fondap (No 15090007); Basal Grant CMM Projects.

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