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http://dx.doi.org/10.9710/kjm.2016.32.3.185

The Protostome database (PANM-DB): Version 2.0 release with updated sequences  

Kang, Se Won (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University)
Park, So Young (Biodiversity Conservation & Change Research Division, Nakdonggang National Institute of Biological Resources)
Patnaik, Bharat Bhusan (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University)
Hwang, Hee Ju (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University)
Chung, Jong Min (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University)
Song, Dae Kwon (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University)
Park, Young-Su (Department of Nursing, College of Medicine, Soonchunhyang University)
Lee, Jun Sang (Institute of Environmental Research, Kangwon National University)
Han, Yeon Soo (College of Agriculture and Life Science, Chonnam National University)
Park, Hong Seog (Research Institute, GnC BIO Co., LTD.)
Lee, Yong Seok (Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University)
Publication Information
The Korean Journal of Malacology / v.32, no.3, 2016 , pp. 185-188 More about this Journal
Abstract
PANM-DB (version 1.0) was constructed as a web-based interface for the analysis and annotation of Next-Generation Sequencing (NGS) data of Mollusca, Arthropoda, and Nematoda. The database collected the sequences of Protostomes (Mollusca, Arthropoda, and Nematoda) from the NCBI Taxonomy Browser, and the same were compiled in a multi-FASTA format and stored using the formatdb program. This improved the processing of the RNA-seq sequences in terms of speed and hit percentage. PANM-DB has been successfully used for the transcriptome annotation of butterfly, land snail, and other commercial mollusca. We have improved the database by updating the same with new sequences and version 2.0 contains a total of 7,571,246 protein sequences (two times more as compared to version 1.0). Furthermore, the updated version contains the Cephalopoda database. The constructed web interface is available that independently analyses following these updates that is an improvement of the mollusks BLAST server. The updated version of PANM-DB will be helpful for the analysis of the NGS based sequencing data of non-model species, especially Mollusca, Arthropoda, Nematoda.
Keywords
PANM-DB; Arthropoda; Nematoda; Mollusks; Cephalopoda;
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Times Cited By KSCI : 4  (Citation Analysis)
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