MetWAMer: eukaryotic translation initiation site prediction
Article Quality & Performance Metrics
Readership in this journal
PopularRanked #100 of 983 articles by views in BMC Bioinformatics
Bar heights use a square-root scale. Only the 120 most-read articles are drawn; the journal has 983 in total.
Mint this article as an NFT
Not yet mintedCreate a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.
Abstract
Abstract
Background
Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations.
Results
MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage.
Conclusion
We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.
| Reference Key |
volker2008metwamerbmc
Use this key to autocite in the manuscript while using
SciMatic Manuscript Manager or Thesis Manager
|
|---|---|
| Authors | |
| Journal | BMC Bioinformatics |
| Year | 2008 |
| DOI |
DOI not found
|
| URL | |
| Keywords |
Biology (General)
Medicine
Materials of engineering and construction. Mechanics of materials
Electrical engineering. Electronics. Nuclear engineering
Computer applications to medicine. Medical informatics
environmental sciences
education (general)
management. industrial management
special aspects of education
computer engineering. computer hardware
electronic computers. computer science
|
Citations
No citations found. To add a citation, contact the admin at info@scimatic.org
ZincirX productsfrom the team behind Journament
-
PatentYazar
Patent drafts for the EPO, USPTO and TürkPatent
From inventor notes to a DOCX draft: description, claims, abstract. The machine drafts, the attorney signs.
See how it works (opens in a new tab) -
Projenator
Have a project idea? Score and plan it with AI
AI scores your idea in five dimensions and builds a phased plan. Your first project is free, no card needed.
Start your first project (opens in a new tab)
Cookies
We use strictly necessary cookies to run the site and keep you signed in. With your permission we would also use Google Analytics to see how the site is used, and Google AdSense to show ads on journal and article pages. Both stay off unless you accept, and you can change your mind at any time. How we use cookies · KVKK notice (Türkiye)
Cookie settings
Comments
No comments yet. Be the first to comment on this article.