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

Author:
  • Björn Canbäck
  • Carl André
  • Juan Galindo
  • Kerstin Johannesson-Andersson
  • Tomas Johansson
  • Marina Panova
  • Anders Tunlid
  • Roger Butlin
Publishing year: 2012
Language: English
Pages: 142-148
Publication/Series: Molecular Ecology Resources
Volume: 12
Document type: Journal article
Publisher: Wiley-Blackwell

Abstract english

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/.

Keywords

  • Biological Sciences
  • ecotype
  • EST database
  • Littorina saxatilis
  • model organism
  • speciation

Other

Published
  • Genome ecology of ectomycorrhizal fungi
  • Microbial Ecology
  • ISSN: 1755-098X
Björn Canbäck
E-mail: bjorn [dot] canback [at] biol [dot] lu [dot] se

Senior lecturer

Molecular Cell Biology

+46 46 222 94 19

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