BLAST databases

The following sequence databases can be searched HERE using BLAST+.

Alvinella pomepjana Transcripts

All contigs from a velvet/oases/cap3 assembly of Illumina, Sanger and Roche 454 Alvinella pompejana sequences from Holder et al. and all ESTs available in NCBI as of April 2011.
Contains 97,285 sequences.
Reference: Holder et al, 2013
 

Alvinella pompejana Predicted Proteins

All predicted Alvinella pompejana proteins (>60 amino acids) derived from the Alvinella pompejana Transcripts dataset using ESTSCAN.
Contains 42,665 sequences.
Reference: Holder et al, 2013
 

Alvinella pompejana MPI ESTs

Alvinella pompejana EST sequences from the MPI EST collection. The library was cloned in pENTR222.1 and sequenced with the M13-FP primer. Base calling and vector trimming were done with Phred and Cross-match.
Contains 10,063 sequences.
Reference: Holder et al, 2013
 

Platynereis_dumerilii MPI ESTs

Platynereis dumerilii EST sequences from the MPI EST collection. The library was cloned in pCMV-Sport6 and sequenced with the SP6 primer. Base calling and vector trimming were done with Phred and Cross-match.
Contains 83,425 sequences.
 

Platynereis dumerilii transcriptome assembly version 1

Transcriptome assembly version 1 of Platynereis dumerilii. The assembly was done with clc and cap3. Each sequence is annotated with its best hit in the SwissProt database. Sequences shorter than 200 nucleotides were removed.
Contains 351,625 sequences.
Reference: Conzelmann et al., 2013
 

Platynereis dumerilii transcriptome assembly version 2

Transcriptome assembly version 2 of Platynereis dumerilii. The assembly was done with trinity and cap3. Each sequence is annotated with its best hit in the SwissProt database.
Contains 611,345 sequences.
Reference: unpublished
 

Platynereis dumerilii transcriptome v021

Transcriptome assembly of Platynereis dumerilii.
Reference: Mutemi at al. 2024
 

Platynereis dumerilii genome v021

Genome assembly Platynereis dumerilii.
Reference: Mutemi at al. 2024
 

References

1. Holder T, Basquin C, Ebert J, Randel N, Jollivet D, Conti E, Jékely G & Bono F (2013) Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a measure of eukaryotic thermostability. BMC Genomics 8, 2. [Article]
    
2. Conzelmann M, Williams EA, Krug K, Franz-Wachtel M, Macek M & Jékely G (2013) The neuropeptide complement of the marine annelid Platynereis dumerilii. BMC Genomics 14, 906. [Article]


3. Mutemi KN, Simakov O, Pan L, Santangeli L, Null R, Handberg-Thorsager M, Cossermelli Vellutini B, Larsson T, Savage E, Osuna Lopez M, Hercog R, Provaznik J, Ordoñez-Rueda D, Azevedo N, Gazave E, Vervoort M, Tomancak P, Tan W, Winkler S, Benes V, Hui J, Helm C, Özpolat BD, Arendt D (2024) A genome resource for the marine annelid Platynereis dumerilii. bioRxiv 2024.06.21.600153. [Article]