Databases and software for the comparison of prokaryotic genomes.
نویسندگان
چکیده
The explosion in the number of complete genomes over the past decade has spawned a new and exciting discipline, that of comparative genomics. To exploit the full potential of this approach requires the development of novel algorithms, databases and software which are sophisticated enough to draw meaningful comparisons between complete genome sequences and are widely accessible to the scientific community at large. This article reviews progress towards the development of computational tools and databases for organizing and extracting biological meaning from the comparison of large collections of genomes.
منابع مشابه
GeneMarkS-2: Raising Standards of Accuracy in Gene Recognition
Motivation: Ab initio gene prediction in prokaryotic genomes is supposed to be so accurate that RNASeq data are rarely produced to bring in an additional layer of evidence. In 2016 more than 60,000 prokaryotic genomes were re-annotated by the NCBI pipeline. Given the sheer volume of prokaryotic DNA data flowing from next generation sequencing facilities into genome databases, the annotation acc...
متن کاملSolving the Problem: Genome Annotation Standards before the Data Deluge
The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimen...
متن کاملMyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation
MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.
متن کاملA web-based software system for dynamic gene cluster comparison across multiple genomes
SUMMARY Investigating the conservation of gene clusters across multiple genomes has become a standard practice in the era of comparative genomics. However, all existing software and databases rely heavily on pre-computation to identify homologous genes by genome-wide comparisons. Such pre-computing strategies lack accuracy and updating the data is computationally intensive. Since most molecular...
متن کاملThe low incidence of diversity-generating retroelements in sequenced genomes
The insertion of a retrotransposable element is usually associated with adverse or, at best, neutral effects on the host. Diversity-generating retroelements (DGRs) are the first elements that seem to offer a direct selective advantage to their phage or prokaryote host by exact replacement of a short, defined region of a host gene with a hypermutated variant. In a previous study, we presented th...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Microbiology
دوره 151 Pt 7 شماره
صفحات -
تاریخ انتشار 2005