CycADS: an annotation database system to ease the development and update of BioCyc databases

Abstract

In recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. The BioCyc databases offer a framework for the integrated analysis of metabolic networks. The Pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a GenBank file. To allow the easy creation and update of a BioCyc database starting from the multiple genome annotation resources available over time, we have developed an ad hoc data management system that we called Cyc Annotation Database System (CycADS). CycADS is centred on a specific database model and on a set of Java programs to import, filter and export relevant information. Data from GenBank and other annotation sources (including for example: KAAS, PRIAM, Blast2GO and PhylomeDB) are collected into a database to be subsequently filtered and extracted to generate a complete annotation file. This file is then used to build an enriched BioCyc database using the PathoLogic program of Pathway Tools. The CycADS pipeline for annotation management was used to build the AcypiCyc database for the pea aphid (Acyrthosiphon pisum) whose genome was recently sequenced. The AcypiCyc database webpage includes also, for comparative analyses, two other metabolic reconstruction BioCyc databases generated using CycADS: TricaCyc for Tribolium castaneum and DromeCyc for Drosophila melanogaster. Linked to its flexible design, CycADS offers a powerful software tool for the generation and regular updating of enriched BioCyc databases. The CycADS system is particularly suited for metabolic gene annotation and network reconstruction in newly sequenced genomes. Because of the uniform annotation used for metabolic network reconstruction, CycADS is particularly useful for comparative analysis of the metabolism of different organisms.Database URL: http://www.cycadsys.org

Tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development

“…To explore the general metabolic changes that take place during the parthenogenetic development of the pea aphid, we analyzed the relevant genes (Additional file 1: Table S1) using the annotations available in the AcypiCyc database, which contains the global reconstruction of the metabolic network of the pea aphid [56]. At least one enzyme-coding gene showed significant differential expression for 43, 74 and 90 pathways in the EE-IE, IE-LE and LE-L1 comparisons, respectively (Additional file 5: Table S5).…”

“…This additional in silico analysis confirmed the hypothetical role of these four genes in coding the enzymes catalyzing the aspartate, tyrosine and aromatic amino acids transamination reactions. The two more specific annotations of PRIAM are not included in the AcypiCyc database as they did not pass the cut-off point applied in the generation of the database using CycADS [56]. Finally, we analyzed the gene structure and the genome organization of the four genes encoding for the enzyme aspartate transaminase (E.C.…”

“…LE and a reduction in expression in the passage from LE to L1 (Additional file 10: Table S11A). Multiple pea aphid proteins have been annotated as having the enzymatic activity DOPA decarboxylase (EC 4.1.1.28) in AcypiCyc and, among them, the gene ACYPI009626 received the highest annotation score [56]. It was also seen to be significantly up-regulated in the LE embryo group, compared to IE, and down-regulated in the transition from LE to L1 (Additional file 10: Table S11A).…”

FastAnnotator- an efficient transcript annotation web tool

“…Bioinformatics analyses performed after sequencing, including assembly, functional annotation and classification, are becoming increasingly important. Several annotation pipelines have been developed, such as CycADS, PRIAM and Blast2GO [4-6], which can provide putative functions for a transcript based on sequence similarity to known genes. Although these tools are useful for understanding the newly explored sequences, they usually contain many manual steps and often are not easy to implement for biologists who are unfamiliar with the command line inputs.…”

“…The majority of established annotation methods utilize these functional annotation systems and transfer functional annotations among sequences based on sequence similarity or pattern searches. For example, the CycADS pipeline integrates multiple annotation tools and databases [4]; PRIAM identifies enzyme functions based on profiles constructed from known enzymes [6]; and Blast2GO annotates gene functions based on a combinations of various annotation methods [5]. The strategy of annotation transfer has been shown to work well and is frequently employed.…”