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ISSN : 1225-3480
A stand-alone BLAST server is available that provides a convenient and amenable platform for the analysis of molluscan sequence information especially the EST sequences generated by traditional sequencing methods. However, it is found that the server has limitations in the annotation of molluscan sequences generated using next-generation sequencing (NGS) platforms due to inconsistencies in molluscan sequence available at NCBI. We constructed a web-based interface for a new stand-alone BLAST, called PANM-DB (Protostome DB) for the analysis of molluscan NGS data. The PANM-DB includes the amino acid sequences from the protostome groups-Arthropoda, Nematoda, and Mollusca downloaded from GenBank with the NCBI taxonomy Browser. The sequences were translated into multi-FASTA format and stored in the database by using the formatdb program at NCBI. PANM-DB contains 6% of NCBInr database sequences (as of 24-06-2015), and for an input of 10,000 RNA-seq sequences the processing speed was 15 times faster by using PANM-DB when compared with NCBInr DB. It was also noted that PANM-DB show two times more significant hits with diverse annotation profiles as compared with Mollusks DB. Hence, the construction of PANM-DB is a significant step in the annotation of molluscan sequence information obtained from NGS platforms. The PANM-DB is freely downloadable from the web-based interface (Malacological Society of Korea, http://malacol.or/kr/blast) as compressed file system and can run on any compatible operating system.
Baker, M.. (2010). Next-generation sequencing: adjusting to data overload. Nature Methods, 7, 495-499. 10.1038/nmeth0710-495.
Bao, H., Guo, H., Wang, J., Zhou, R., Lu, X. and Shi, S.. (2009). MapView: visualization of short reads alignment on a desktop computer. Bioinformatics, 25, 1554-1555. 10.1093/bioinformatics/btp255.
Harrison, N. and Kidner, C.A.. (2011). Next-generation sequencing and systematics: What can a billion base pairs of DNA sequences data do to you?. Taxon, 60, 1552-1566.
Jeong, J.E., Kang, S.W., Hwang, H.J., Chae, S-H., Patnaik, B.B., Han, Y.S., Lee, J.B., Jo, Y.H., Lee, B.L., Seog, D-H. and Lee, Y.S.. (2013). Expressed sequence tags (ESTs) analysis of Tenebrio molitor larvae. Entomological Research, 43, 168-176. 10.1111/1748-5967.12019.
Jeong, J.E., Patnaik, B.B., Kang, S.W., Hwang, H-J., Park, S.Y., Wang, T.H., Park, E.B., Lee, J.B., Nam, M-M., Jo, Y.H., Han, Y.S., Lee, J-S., Park, H.S. and Lee, Y.S.. (2015). Characterization of Physa acuta expressed sequence tags and transcript mining following cadmium exposure. Genes and Genomics, . 10.1007/s13258-015-0334-x.
Kang, S.W., Hwang, H.J., Park, S.Y., Wang, T.H., Park, E.B., Lee, T.H., Hwang, U.W., Lee, J.S., Park, H.S., Han, Y.S., Lim, C.E., Kim, S. and Lee, Y.S.. (2014). Mollusks sequence database: Version II. Korean Journal of Malacology, 30, 429-431. 10.9710/kjm.2014.30.4.429.
Kim, K.M., Park, J-H., Bhattacharya, D. and Yoon, H.S.. (2014). Applications of next-generation sequencing to unravelling the evolutionary history of algae. International Journal of Systematic and Evolutionary Microbiology, 64, 333-345. 10.1099/ijs.0.054221-0.
Lee, Y-S., Jo, Y-H., Kim, D-S., Kim, D-W., Kim, M-Y., Choi, S-H., Yon, J-O., Byun, I-S., Kang, B-R., Jeong, K-H. and Park, H-S.. (2004). Construction of BLAST server for Mollusks. Korean Journal of Malacology, 20, 165-169.
Mardis, E.R.. (2013). Next-Generation Sequencing Platforms. Annual Review of Analytical Chemistry, 6, 287-303. 10.1146/annurev-anchem-062012-092628.
Riesgo, A., Andrade, S.C.S., Sharma, P.P., Novo, M., Perez-Porro, A.R., Vahtera, V., Gonzalez, V.L., Kawauchi, G.Y. and Giribet, G.. (2012). Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Frontiers in Zoology, 9, 33. 10.1186/1742-9994-9-33.
Sanger, F., Nicklen, S. and Coulson, A.R.. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of National Academy of Sciences, USA, 74, 5463-5467. 10.1073/pnas.74.12.5463.
Tsiliki, G., Tsaramirsis, K. and Kossida, S.. (2014). AmalgamScope: Merging annotations data across the Human genome. BioMed Research International, .
Zhu, Z., Niu, B., Chen, J., Wu, S., Sun, S. and Li, W.. (2013). MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. Bioinformatics, 29, 122-123. 10.1093/bioinformatics/bts567.
