JOURNAL BROWSE
Search
Advanced SearchSearch Tips
Construction of PANM Database (Protostome DB) for rapid annotation of NGS data in Mollusks
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
  • Journal title : The Korean Journal of Malacology
  • Volume 31, Issue 3,  2015, pp.243-247
  • Publisher : The Malacological Society of Korea
  • DOI : 10.9710/kjm.2015.31.3.243
 Title & Authors
Construction of PANM Database (Protostome DB) for rapid annotation of NGS data in Mollusks
Kang, Se Won; Park, So Young; Patnaik, Bharat Bhusan; Hwang, Hee Ju; Kim, Changmu; Kim, Soonok; Lee, Jun Sang; Han, Yeon Soo; Lee, Yong Seok;
  PDF(new window)
 Abstract
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.
 Keywords
PANM-DB;protostome;mollusks;NCBInr;next-generation sequencing;
 Language
English
 Cited by
1.
연체동물 NGS 데이터 분석을 위한 PANM 데이터베이스 업데이트 (Version II),강세원;박소영;;황희주;정종민;송대권;박영수;이준상;한연수;박홍석;이용석;

한국패류학회지, 2016. vol.32. 3, pp.185-188 crossref(new window)
2.
CO-I 유전자 기반 국내 유통 Corbicula 속 패류의 종 동정,박소영;강세원;황희주;정종민;송대권;박홍석;한연수;이준상;강정하;이용석;

한국패류학회지, 2016. vol.32. 2, pp.127-131 crossref(new window)
3.
동남아시아 4개국 두족류의 분류 및 계통분류학적 연구,황희주;강세원;박소영;정종민;송대권;박형춘;박홍석;한연수;이준상;이용석;

한국패류학회지, 2016. vol.32. 1, pp.55-62 crossref(new window)
4.
RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862,;;;;;;;;;;;;;;;;

Entomological research, 2016. vol.46. 2, pp.148-161 crossref(new window)
1.
Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery, PLOS ONE, 2016, 11, 2, e0148622  crossref(new windwow)
2.
Assembly, Functional Annotation, and Discovery of SSR Markers, International Journal of Genomics, 2016, 2016, 2314-4378, 1  crossref(new windwow)
3.
Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers, Molecular Genetics and Genomics, 2016, 291, 5, 1999  crossref(new windwow)
4.
Classification and Phylogenetic Studies of Cephalopods from four countries of South-East Asia, The Korean Journal of Malacology, 2016, 32, 1, 55  crossref(new windwow)
5.
A Mitochondiral Cytochrome Oxidase I gene based identification of Corbicula ssp. commercially available in South Korea, The Korean Journal of Malacology, 2016, 32, 2, 127  crossref(new windwow)
6.
Felder, 1862, Entomological Research, 2016, 46, 2, 148  crossref(new windwow)
7.
Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery, Genes, 2016, 7, 10, 35  crossref(new windwow)
8.
Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery, Genes, 2016, 7, 12, 114  crossref(new windwow)
 References
1.
Baker, M. (2010) Next-generation sequencing: adjusting to data overload. Nature Methods, 7: 495-499. crossref(new window)

2.
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. crossref(new window)

3.
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.

4.
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. crossref(new window)

5.
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. doi:10.1007/s13258-015-0334-x. crossref(new window)

6.
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. crossref(new window)

7.
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. crossref(new window)

8.
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.

9.
Mardis, E.R. (2013) Next-Generation Sequencing Platforms. Annual Review of Analytical Chemistry, 6: 287-303. crossref(new window)

10.
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. crossref(new window)

11.
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. crossref(new window)

12.
Tsiliki, G., Tsaramirsis, K. and Kossida, S. (2014) AmalgamScope: Merging annotations data across the Human genome. BioMed Research International, Article ID 893501.

13.
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. crossref(new window)