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

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The Littorina sequence database (LSD) - an online resource for genomic data. / Canbäck, Björn; André, Carl; Galindo, Juan; Johannesson-Andersson, Kerstin; Johansson, Tomas; Panova, Marina; Tunlid, Anders; Butlin, Roger.

I: Molecular Ecology Resources, Vol. 12, 2012, s. 142-148.

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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Canbäck, Björn ; André, Carl ; Galindo, Juan ; Johannesson-Andersson, Kerstin ; Johansson, Tomas ; Panova, Marina ; Tunlid, Anders ; Butlin, Roger. / The Littorina sequence database (LSD) - an online resource for genomic data. I: Molecular Ecology Resources. 2012 ; Vol. 12. s. 142-148.

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TY - JOUR

T1 - The Littorina sequence database (LSD) - an online resource for genomic data.

AU - Canbäck, Björn

AU - André, Carl

AU - Galindo, Juan

AU - Johannesson-Andersson, Kerstin

AU - Johansson, Tomas

AU - Panova, Marina

AU - Tunlid, Anders

AU - Butlin, Roger

PY - 2012

Y1 - 2012

N2 - 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/.

AB - 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/.

KW - ecotype

KW - EST database

KW - Littorina saxatilis

KW - model organism

KW - speciation

U2 - 10.1111/j.1755-0998.2011.03042.x

DO - 10.1111/j.1755-0998.2011.03042.x

M3 - Article

VL - 12

SP - 142

EP - 148

JO - Molecular Ecology Resources

T2 - Molecular Ecology Resources

JF - Molecular Ecology Resources

SN - 1755-098X

ER -