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The Littorina sequence database (LSD) - an online resource for genomic data.

Canbäck, Björn LU ; André, Carl; Galindo, Juan; Johannesson-Andersson, Kerstin LU ; Johansson, Tomas LU ; Panova, Marina; Tunlid, Anders LU and Butlin, Roger (2012) In Molecular Ecology Resources 12. p.142-148
Abstract
We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147 491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26 537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt... (More)
We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147 491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26 537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
ecotype, EST database, Littorina saxatilis, model organism, speciation
in
Molecular Ecology Resources
volume
12
pages
142 - 148
publisher
Wiley-Blackwell
external identifiers
  • wos:000298585000017
  • pmid:21707958
  • scopus:83955165941
ISSN
1755-098X
DOI
10.1111/j.1755-0998.2011.03042.x
project
Genome ecology of ectomycorrhizal fungi
language
English
LU publication?
yes
id
6a3046b2-cf9f-4f57-8ef5-ffb18bdfacd7 (old id 2007700)
date added to LUP
2011-08-22 12:26:31
date last changed
2017-01-01 03:59:25
@article{6a3046b2-cf9f-4f57-8ef5-ffb18bdfacd7,
  abstract     = {We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147 491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26 537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.},
  author       = {Canbäck, Björn and André, Carl and Galindo, Juan and Johannesson-Andersson, Kerstin and Johansson, Tomas and Panova, Marina and Tunlid, Anders and Butlin, Roger},
  issn         = {1755-098X},
  keyword      = {ecotype,EST database,Littorina saxatilis,model organism,speciation},
  language     = {eng},
  pages        = {142--148},
  publisher    = {Wiley-Blackwell},
  series       = {Molecular Ecology Resources},
  title        = {The Littorina sequence database (LSD) - an online resource for genomic data.},
  url          = {http://dx.doi.org/10.1111/j.1755-0998.2011.03042.x},
  volume       = {12},
  year         = {2012},
}