Engineering topics

Disz, Terry

Publications and source records attributed to Disz, Terry.

5 records

DOE OSTI2015

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast. nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Real Time Metagenomics: Using k-mers to annotate metagenomes

Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2011

Grounding annotations in published literature with an emphasis on the functional roles used in metabolic models

Accurate genome annotations in databases are a critical resource available to the scientific community for analysis and research. Inaccurate and inconsistent annotations exist as a result of errors generated from mass automated annotation, and currently act as a barrier to the application of bioinformatics. The purpose of this effort was to improve the SEED by improving the connection of functional roles to literature references. Direct literature references (DLits), found through searches of PubMed and other online databases such as SwissProt, were attached to protein sequences within the PubSEED to provide literature support for the roughly 2,500 distinct functional roles used to construct metabolic models within the Model SEED. Only DLits in which a researcher asserted the function of a protein were attached to sequences. Starting from a list of 1,072 functional roles that did not previously have DLit support, we were able to connect sequences to literature for 655 functional roles, at least 484 of which were in the original list of unsupported roles. When added to the existing set of sequences having DLits, the resulting set of DLit-sequence pairs (the foundation set) now connects approximately 4,300 DLits to approximately 5,600 distinct protein sequences obtained from approximately 16,000 genes (some of these genes have identical protein sequences). From the foundation set, we construct projection sets such that each set contains one member of the foundation set and projections of its functional role onto similar genes. The projection sets revealed 120 inconsistent annotations within the SEED. Two types of inconsistencies were corrected through manual annotation in the PubSEED: instances in which two identical protein sequences had been annotated with different functions, and instances when projected functions contradicted previous annotations. 26,785 changes to gene function assignment, 219 of which were to previously uncharacterized proteins, resulted in a more consistent and accurate set of input data from which to construct revised metabolic models within the Model SEED.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2010

Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

Background: The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. Results: The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. Conclusions: We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

59 BASIC BIOLOGICAL SCIENCES↗