Dataset Information

IPathCons and iPathDB: an improved insect pathway construction tool and the database.

ABSTRACT: 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/

SUBMITTER: Zhang Z

PROVIDER: S-EPMC4227299 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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iPathCons and iPathDB: an improved insect pathway construction tool and the database.

Zhang Zan Z Yin Chuanlin C Liu Ying Y Jie Wencai W Lei Wenjie W Li Fei F

Database : the journal of biological databases and curation 20141111

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 de ...[more]

PMID: 25388589

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Project description:BackgroundAligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments, however, are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Automatically created ncRNA alignments often need manual corrections, yet this manual refinement is tedious and error-prone.ResultsWe present an extended version of CONSTRUCT, a semi-automatic, graphical tool suitable for creating RNA alignments correct in terms of both consensus sequence and consensus structure. To this purpose CONSTRUCT combines sequence alignment, thermodynamic data and various measures of covariation. One important feature is that the user is guided during the alignment correction step by a consensus dotplot, which displays all thermodynamically optimal base pairs and the corresponding covariation. Once the initial alignment is corrected, optimal and suboptimal secondary structures as well as tertiary interaction can be predicted. We demonstrate CONSTRUCT's ability to guide the user in correcting an initial alignment, and show an example for optimal secondary consensus structure prediction on very hard to align SECIS elements. Moreover we use CONSTRUCT to predict tertiary interactions from sequences of the internal ribosome entry site of CrP-like viruses. In addition we show that alignments specifically designed for benchmarking can be easily be optimized using CONSTRUCT, although they share very little sequence identity.ConclusionCONSTRUCT's graphical interface allows for an easy alignment correction based on and guided by predicted and known structural constraints. It combines several algorithms for prediction of secondary consensus structure and even tertiary interactions. The CONSTRUCT package can be downloaded from the URL listed in the Availability and requirements section of this article.

Dataset Information

IPathCons and iPathDB: an improved insect pathway construction tool and the database.

Publications

iPathCons and iPathDB: an improved insect pathway construction tool and the database.

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