Patella vulgata and Spirobranchus (Pomatoceros) lamarcki genonme and transcriptome assemblies.
The data are associated with the publication: Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). The data were generated to allow genome-wide predi...
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| Format: | Dataset |
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University of Oxford
2015
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| _version_ | 1826276025901776896 |
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| author | Shimeld, S |
| author_facet | Shimeld, S |
| author_sort | Shimeld, S |
| collection | OXFORD |
| description | The data are associated with the publication: Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). The data were generated to allow genome-wide prediction of microRNA genes and hence allow hypotheses concerning microRNA gene loss and homoplasy to be tested.
The data are transcriptome and genome assemblies built from raw sequence data derived from the Illumina GAII and Illumina Hi-Seq2000 sequencing platforms. The raw data pertaining to the genome assemblies for both species are available from the public NCBI Short Read Archive under accession numbers NCBI SRA SRP055158 and SRP055157. Additional information on the transcriptome assemblies and associated data can be found in Werner et al (2012) Mar. Biotechnol. DOI 10.1007/s10126-012-9481-0., and in Kenny and Shimeld (2012) Dev. Genes. Evol. DOI 10.1007/s00427-012-0416-6.
The data are all is fasta format (with files appended with .fas or .fa). One is zipped.
Authors: Nathan J Kenny, Erica K O Namigai, Ferdinand Marlétaz, Jerome H.L. Hui, Sebastian M Shimeld.
Patella vulgata
Transcriptome
File: PatellaContigsFinalContaminatedRemovedNucleotide.fas
Genome
File: abyss57mer300bptrim.fa
Spirobranchus (Pomatoceros) lamarcki
Transcriptome
File: PomatocerosContigsFinalRenamed(1).fas
Genome
File: poma_61_contigs.fa
(This is the Velvet 61kmer assembly that has appears to be the best as judged by N50).
File: pomsoap2quake-K51.scafSeq.gz
(This is the SOAP 51kmer assembly of Quake-modified data that was used for miRNA prediction in Kenny et al).
Geographical location or coverage of the data:
Biological samples used to generate all datasets were collected from Tinside beach, Plymouth, UK
Multiple software packages (SOAP, ABYSS, VELVET) have been used to build these assemblies. The package used in each case is described in these publications, and is indicated in the file names. All assemblies are in FASTA format. |
| first_indexed | 2024-03-06T23:07:46Z |
| format | Dataset |
| id | oxford-uuid:6471e7d4-dd34-4eb3-883f-a5c438f11741 |
| institution | University of Oxford |
| last_indexed | 2024-03-06T23:07:46Z |
| publishDate | 2015 |
| publisher | University of Oxford |
| record_format | dspace |
| spelling | oxford-uuid:6471e7d4-dd34-4eb3-883f-a5c438f117412022-03-26T18:18:59ZPatella vulgata and Spirobranchus (Pomatoceros) lamarcki genonme and transcriptome assemblies.Datasethttp://purl.org/coar/resource_type/c_ddb1uuid:6471e7d4-dd34-4eb3-883f-a5c438f11741ORA DepositUniversity of Oxford2015Shimeld, SThe data are associated with the publication: Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). The data were generated to allow genome-wide prediction of microRNA genes and hence allow hypotheses concerning microRNA gene loss and homoplasy to be tested. The data are transcriptome and genome assemblies built from raw sequence data derived from the Illumina GAII and Illumina Hi-Seq2000 sequencing platforms. The raw data pertaining to the genome assemblies for both species are available from the public NCBI Short Read Archive under accession numbers NCBI SRA SRP055158 and SRP055157. Additional information on the transcriptome assemblies and associated data can be found in Werner et al (2012) Mar. Biotechnol. DOI 10.1007/s10126-012-9481-0., and in Kenny and Shimeld (2012) Dev. Genes. Evol. DOI 10.1007/s00427-012-0416-6. The data are all is fasta format (with files appended with .fas or .fa). One is zipped. Authors: Nathan J Kenny, Erica K O Namigai, Ferdinand Marlétaz, Jerome H.L. Hui, Sebastian M Shimeld. Patella vulgata Transcriptome File: PatellaContigsFinalContaminatedRemovedNucleotide.fas Genome File: abyss57mer300bptrim.fa Spirobranchus (Pomatoceros) lamarcki Transcriptome File: PomatocerosContigsFinalRenamed(1).fas Genome File: poma_61_contigs.fa (This is the Velvet 61kmer assembly that has appears to be the best as judged by N50). File: pomsoap2quake-K51.scafSeq.gz (This is the SOAP 51kmer assembly of Quake-modified data that was used for miRNA prediction in Kenny et al). Geographical location or coverage of the data: Biological samples used to generate all datasets were collected from Tinside beach, Plymouth, UK Multiple software packages (SOAP, ABYSS, VELVET) have been used to build these assemblies. The package used in each case is described in these publications, and is indicated in the file names. All assemblies are in FASTA format. |
| spellingShingle | Shimeld, S Patella vulgata and Spirobranchus (Pomatoceros) lamarcki genonme and transcriptome assemblies. |
| title | Patella vulgata and Spirobranchus (Pomatoceros) lamarcki genonme and transcriptome assemblies. |
| title_full | Patella vulgata and Spirobranchus (Pomatoceros) lamarcki genonme and transcriptome assemblies. |
| title_fullStr | Patella vulgata and Spirobranchus (Pomatoceros) lamarcki genonme and transcriptome assemblies. |
| title_full_unstemmed | Patella vulgata and Spirobranchus (Pomatoceros) lamarcki genonme and transcriptome assemblies. |
| title_short | Patella vulgata and Spirobranchus (Pomatoceros) lamarcki genonme and transcriptome assemblies. |
| title_sort | patella vulgata and spirobranchus pomatoceros lamarcki genonme and transcriptome assemblies |
| work_keys_str_mv | AT shimelds patellavulgataandspirobranchuspomatoceroslamarckigenonmeandtranscriptomeassemblies |