The Protostome database (PANM-DB): Version 2.0 release with updated sequences
Se Won Kang, So Young Park, Bharat Bhusan Patnaik, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Young-Su Park, Jun Sang Lee, Yeon Soo Han, Hong Seog Park and Yong Seok Lee
Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam 31538, Korea Biodiversity Conservation & Change Research Division, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongb
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 transcript-xome 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. (
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