Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource
Background To identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries...
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ftoslouniv:oai:www.duo.uio.no:10852/46600 2023-05-15T15:30:53+02:00 Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource Adzhubei, Alexei A Vlasova, Anna V Hagen-Larsen, Heidi Ruden, Torgeir A Laerdahl, Jon K Høyheim, Bjørn 2007 http://hdl.handle.net/10852/46600 http://urn.nb.no/URN:NBN:no-50786 https://doi.org/10.1186/1471-2164-8-209 eng eng http://urn.nb.no/URN:NBN:no-50786 BMC Genomics. 2007 Jul 02;8(1):209 http://hdl.handle.net/10852/46600 http://dx.doi.org/10.1186/1471-2164-8-209 URN:NBN:no-50786 Fulltext https://www.duo.uio.no/bitstream/handle/10852/46600/1/12864_2007_Article_922.pdf Adzhubei et al. Attribution 2.0 Generic http://creativecommons.org/licenses/by/2.0/ CC-BY Journal article Tidsskriftartikkel Peer reviewed PublishedVersion 2007 ftoslouniv https://doi.org/10.1186/1471-2164-8-209 2020-06-21T08:48:53Z Background To identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries allow identification of a large number of different transcripts and can provide valuable information on genes expressed in a particular tissue at a specific developmental stage. This data is important in constructing a microarray chip, identifying SNPs in coding regions, and for future identification of genes in the whole genome sequence. An important factor that determines the usefulness of generated data for biologists is efficient data access. Public searchable databases play a crucial role in providing such service. Description Twenty-three Atlantic salmon cDNA libraries were constructed from 15 tissues, yielding nearly 155,000 clones. From these libraries 58,109 ESTs were generated, of which 57,212 were used for contig assembly. Following deletion of mitochondrial sequences 55,118 EST sequences were submitted to GenBank. In all, 20,019 unique sequences, consisting of 6,424 contigs and 13,595 singlets, were generated. The Norwegian Salmon Genome Project Database has been constructed and annotation performed by the annotation transfer approach. Annotation was successful for 50.3% (10,075) of the sequences and 6,113 sequences (30.5%) were annotated with Gene Ontology terms for molecular function, biological process and cellular component. Conclusion We describe the construction of cDNA libraries from juvenile/pre-smolt Atlantic salmon (Salmo salar), EST sequencing, clustering, and annotation by assigning putative function to the transcripts. These sequences represents 97% of all sequences submitted to GenBank from the pre-smoltification stage. The data has been grouped into datasets according to its source and type of annotation. Various data query options are offered including searches on function assignments and Gene Ontology terms. Data delivery options include summaries for the datasets and their annotations, detailed self-explanatory annotations, and access to the original BLAST results and Gene Ontology annotation trees. Potential presence of a relatively high number of immune-related genes in the dataset was shown by annotation searches. Article in Journal/Newspaper Atlantic salmon Salmo salar Universitet i Oslo: Digitale utgivelser ved UiO (DUO) BMC Genomics 8 1 209 |
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Open Polar |
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Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
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ftoslouniv |
language |
English |
description |
Background To identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries allow identification of a large number of different transcripts and can provide valuable information on genes expressed in a particular tissue at a specific developmental stage. This data is important in constructing a microarray chip, identifying SNPs in coding regions, and for future identification of genes in the whole genome sequence. An important factor that determines the usefulness of generated data for biologists is efficient data access. Public searchable databases play a crucial role in providing such service. Description Twenty-three Atlantic salmon cDNA libraries were constructed from 15 tissues, yielding nearly 155,000 clones. From these libraries 58,109 ESTs were generated, of which 57,212 were used for contig assembly. Following deletion of mitochondrial sequences 55,118 EST sequences were submitted to GenBank. In all, 20,019 unique sequences, consisting of 6,424 contigs and 13,595 singlets, were generated. The Norwegian Salmon Genome Project Database has been constructed and annotation performed by the annotation transfer approach. Annotation was successful for 50.3% (10,075) of the sequences and 6,113 sequences (30.5%) were annotated with Gene Ontology terms for molecular function, biological process and cellular component. Conclusion We describe the construction of cDNA libraries from juvenile/pre-smolt Atlantic salmon (Salmo salar), EST sequencing, clustering, and annotation by assigning putative function to the transcripts. These sequences represents 97% of all sequences submitted to GenBank from the pre-smoltification stage. The data has been grouped into datasets according to its source and type of annotation. Various data query options are offered including searches on function assignments and Gene Ontology terms. Data delivery options include summaries for the datasets and their annotations, detailed self-explanatory annotations, and access to the original BLAST results and Gene Ontology annotation trees. Potential presence of a relatively high number of immune-related genes in the dataset was shown by annotation searches. |
format |
Article in Journal/Newspaper |
author |
Adzhubei, Alexei A Vlasova, Anna V Hagen-Larsen, Heidi Ruden, Torgeir A Laerdahl, Jon K Høyheim, Bjørn |
spellingShingle |
Adzhubei, Alexei A Vlasova, Anna V Hagen-Larsen, Heidi Ruden, Torgeir A Laerdahl, Jon K Høyheim, Bjørn Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource |
author_facet |
Adzhubei, Alexei A Vlasova, Anna V Hagen-Larsen, Heidi Ruden, Torgeir A Laerdahl, Jon K Høyheim, Bjørn |
author_sort |
Adzhubei, Alexei A |
title |
Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource |
title_short |
Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource |
title_full |
Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource |
title_fullStr |
Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource |
title_full_unstemmed |
Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource |
title_sort |
annotated expressed sequence tags (ests) from pre-smolt atlantic salmon (salmo salar) in a searchable data resource |
publishDate |
2007 |
url |
http://hdl.handle.net/10852/46600 http://urn.nb.no/URN:NBN:no-50786 https://doi.org/10.1186/1471-2164-8-209 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
http://urn.nb.no/URN:NBN:no-50786 BMC Genomics. 2007 Jul 02;8(1):209 http://hdl.handle.net/10852/46600 http://dx.doi.org/10.1186/1471-2164-8-209 URN:NBN:no-50786 Fulltext https://www.duo.uio.no/bitstream/handle/10852/46600/1/12864_2007_Article_922.pdf |
op_rights |
Adzhubei et al. Attribution 2.0 Generic http://creativecommons.org/licenses/by/2.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/1471-2164-8-209 |
container_title |
BMC Genomics |
container_volume |
8 |
container_issue |
1 |
container_start_page |
209 |
_version_ |
1766361360862543872 |