iPathCons and iPathDB: an improved insect pathway construction tool and the database.
Insects are one of the most successful animal groups on earth. Some insects, such as the silkworm and honeybee, are beneficial to humans, whereas others are notorious pests of crops. At present, the genomes of 38 insects have been sequenced and made publically available. In addition, the transcriptomes of dozens of insects have been sequenced. As gene data rapidly accumulate, constructing the pathway of molecular interactions becomes increasingly important for entomological research. Here, we developed an improved tool, iPathCons, for knowledge-based construction of pathways from the transcriptomes or the official gene sets of genomes. Considering the high evolution diversity in insects, iPathCons uses a voting system for Kyoto Encyclopedia of Genes and Genomes Orthology assignment. Both stand-alone software and a web server of iPathCons are provided. Using iPathCons, we constructed the pathways of molecular interactions of 52 insects, including 37 genome-sequenced and 15 transcriptome-sequenced ones. These pathways are available in the iPathDB, which provides searches, web server, data downloads, etc. This database will be highly useful for the insect research community. Database URL: http://ento.njau.edu.cn/ipath/
Department of Entomology, College of Plant Protection, Nanjing Agricultural University and The Key laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Agriculture, No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China.
Zan
Z
Zhang
Department of Entomology, College of Plant Protection, Nanjing Agricultural University and The Key laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Agriculture, No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China.
Chuanlin
C
Yin
Department of Entomology, College of Plant Protection, Nanjing Agricultural University and The Key laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Agriculture, No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China.
Ying
Y
Liu
Department of Entomology, College of Plant Protection, Nanjing Agricultural University and The Key laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Agriculture, No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China.
Wencai
W
Jie
Department of Entomology, College of Plant Protection, Nanjing Agricultural University and The Key laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Agriculture, No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China.
Wenjie
W
Lei
Department of Entomology, College of Plant Protection, Nanjing Agricultural University and The Key laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Agriculture, No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China lifei@njau.edu.cn.
Fei
F
Li
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D049750:Genome, Insect / Q000235:genetics*; D007313:Insecta / Q000235:genetics / Q000378:metabolism; D020407:Internet; D012984:Software; D059467:Transcriptome / Q000235:genetics*