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Protocols

SalmoBase specifications

Information


Unique identifier OMICS_19266
Name SalmoBase
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

Maintainer


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Publication for SalmoBase

SalmoBase citations

 (5)
library_books

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry

2018
BMC Genomics
PMCID: 5902856
PMID: 29661132
DOI: 10.1186/s12864-018-4651-8

[…] e (ICSASG_v2) using STAR (v2.5.2a). Raw gene counts per sample were generated from read alignments using HTSeq-count (v0.6.1p1) and the NCBI salmon genome annotation (available for download at http://salmobase.org/Downloads/Salmo_salar-annotation.gff3.gz). The uniquely mapped reads, aligned to exon regions, were counted for each gene in the annotation.For each tissue type (SM, PC, HG), a different […]

library_books

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

2018
PeerJ
PMCID: 5807978
PMID: 29441236
DOI: 10.7717/peerj.4345

[…] ed with this filtering step, e.g., the N10–N50 statistics ().Blastn revealed that the majority of the transcripts had homology with sequences in Atlantic salmon (72% for the NCBI database and 83% for SalmoBase) and rainbow trout (53%). Similar analyses at the protein level (blastx or blastp) found a lower proportion with homology, 43% to 55% depending on the database in the two salmonids and other […]

library_books

Lineage specific rediploidization is a mechanism to explain time lags between genome duplication and evolutionary diversification

2017
Genome Biol
PMCID: 5470254
PMID: 28615063
DOI: 10.1186/s13059-017-1241-z

[…] ely mapped reads were counted using the HTSeq python script [] in combination with a modified RefSeq.gff file. The .gff file was modified to contain the attribute “gene_id” (file accessible at http://salmobase.org/download.html). Expression levels were calculated as counts per million total library counts in EdgeR []. Total library sizes were normalised to account for bias in sample composition us […]

call_split

NFAT5 genes are part of the osmotic regulatory system in Atlantic salmon (Salmo salar)

2017
PMCID: 5292104
PMID: 27330039
DOI: 10.1016/j.margen.2016.06.004
call_split See protocol

[…] ment of predicted amino acid sequences was performed using CLUSTALW2 (http://align.genome.jp) ().Synteny analyses were carried out using the Generic Genome Browser (version 2.55) on SalmoBase (http://salmobase.org/cgi-bin/gb2/gbrowse/salmon_GBrowse_Chr_NCBI/). The data source for the browser was Ssal ICSASG_v2. 100 kbp up- and downstream of each S. salar NFAT5 paralogue were analysed along with th […]

library_books

The complete salmonid IGF IR gene repertoire and its transcriptional response to disease

2016
Sci Rep
PMCID: 5066257
PMID: 27748369
DOI: 10.1038/srep34806

[…] GI 4.2). Salmonid IGF-IR genes were acquired using northern pike IGF-IRa and IGF-IRb amino acid sequences as queries in tBLASTn searches of Atlantic salmon and rainbow trout genome assemblies through SalmoBase (http://salmobase.org/index.php) and the National Animal Genome Research Program (http://www.animalgenome.org/), respectively. Rainbow trout coding sequences were predicted from the correspo […]

Citations

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SalmoBase institution(s)
Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Akershus, Norway
SalmoBase funding source(s)
Supported by the Research Council of Norway, project no. 208481 (ELIXIR.NO).

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