Featured Research

from universities, journals, and other organizations

Protein Misprediction Uncovered By New Technique

Date:
August 28, 2008
Source:
BMC Bioinformatics
Summary:
A new bioinformatics tool is capable of identifying and correcting abnormal, incomplete and mispredicted protein annotations in public databases. The MisPred tool currently uses five principles to identify suspect proteins that are likely to be abnormal or mispredicted.

A new bioinformatics tool is capable of identifying and correcting abnormal, incomplete and mispredicted protein annotations in public databases. The MisPred tool, described today in the open access journal BMC Bioinformatics, currently uses five principles to identify suspect proteins that are likely to be abnormal or mispredicted.

Related Articles


László Patthy led a team from the Institute of Enzymology of the Hungarian Academy of Sciences, Budapest, that developed this new approach. He explained how necessary it is, "Recent studies have shown that a significant proportion of eukaryotic genes are mispredicted at the transcript level. As the MisPred routines are able to detect many of these errors, and may aid in their correction, we suggest that it may significantly improve the quality of protein sequence data based on gene predictions". The MisPred approach promises to save much time and effort that would otherwise be spent in further investigation of erroneously identified genes.

The MisPred approach rates annotations according to five dogmas:

  • Extracellular or transmembrane proteins must have appropriate secretory signals.
  • A protein with intra- and extra-cellular parts must have a transmembrane segment.
  • Extracellular and nuclear domains must not occur in a single protein.
  • The number of amino acid residues in closely related members of a globular domain family must fall into a relatively narrow range.
  • A protein must be encoded by exons located on a single chromosome.

There are some exceptions to these rules, as pointed out by Patthy, "Some secreted proteins may truly lack secretory signal peptides since they are subject to leaderless protein secretion. Similarly, it cannot be excluded at present that transchromosomal chimeras can be formed and may have normal physiological functions. Nevertheless, the fact that MisPred analyses of protein sequences of the Swiss-Prot database identified very few such exceptions indicates that the rules of MisPred are generally valid".

The authors found that the absence of expected signal peptides and violation of domain integrity account for the majority of mispredictions. The authors note that "Interestingly, even the manually curated UniProtKB/Swiss-Prot dataset is contaminated with mispredicted or abnormal proteins, although to a much lesser extent than UniProtKB/TrEMBL or the EnsEMBL or GNOMON predicted entries".


Story Source:

The above story is based on materials provided by BMC Bioinformatics. Note: Materials may be edited for content and length.


Journal Reference:

  1. Alinda Nagy, Hedi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, Laszlo and Laszlo Patthy. Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. BMC Bioinformatics, (in press)

Cite This Page:

BMC Bioinformatics. "Protein Misprediction Uncovered By New Technique." ScienceDaily. ScienceDaily, 28 August 2008. <www.sciencedaily.com/releases/2008/08/080826205930.htm>.
BMC Bioinformatics. (2008, August 28). Protein Misprediction Uncovered By New Technique. ScienceDaily. Retrieved October 25, 2014 from www.sciencedaily.com/releases/2008/08/080826205930.htm
BMC Bioinformatics. "Protein Misprediction Uncovered By New Technique." ScienceDaily. www.sciencedaily.com/releases/2008/08/080826205930.htm (accessed October 25, 2014).

Share This



More Plants & Animals News

Saturday, October 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Deep Sea 'mushroom' Could Be Early Branch on Tree of Life

Deep Sea 'mushroom' Could Be Early Branch on Tree of Life

Reuters - Innovations Video Online (Oct. 24, 2014) — Miniature deep sea animals discovered off the Australian coast almost three decades ago are puzzling scientists, who say the organisms have proved impossible to categorise. Academics at the Natural History of Denmark have appealed to the world scientific community for help, saying that further information on Dendrogramma enigmatica and Dendrogramma discoides could answer key evolutionary questions. Jim Drury has more. Video provided by Reuters
Powered by NewsLook.com
Black Bear Cub Goes Sunday Shopping

Black Bear Cub Goes Sunday Shopping

Reuters - Light News Video Online (Oct. 23, 2014) — Price check on honey? Bear cub startles Oregon drugstore shoppers. Rough Cut (no reporter narration). Video provided by Reuters
Powered by NewsLook.com
Dances With Wolves in China's Wild West

Dances With Wolves in China's Wild West

AFP (Oct. 23, 2014) — One man is on a mission to boost the population of wolves in China's violence-wracked far west. The animal - symbol of the Uighur minority there - is under threat with a massive human resettlement program in the region. Duration: 00:41 Video provided by AFP
Powered by NewsLook.com
Breakfast Debate: To Eat Or Not To Eat?

Breakfast Debate: To Eat Or Not To Eat?

Newsy (Oct. 23, 2014) — Conflicting studies published in the same week re-ignited the debate over whether we should be eating breakfast. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:

Strange & Offbeat Stories

 

Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:  

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile iPhone Android Web
Follow Facebook Twitter Google+
Subscribe RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins