New tool to improve protein database quality control emerges Public databases continue to have abnormal, incomplete and mispredicted genes and proteins in spite of the recent efforts made to improve the computational annotation of genomes. These errors adversely impact the reliability of the databases. But a team of researchers has deve... Public databases continue to have abnormal, incomplete and mispredicted genes and proteins in spite of the recent efforts made to improve the computational annotation of genomes. These errors adversely impact the reliability of the databases. But a team of researchers has developed a new tool offering an efficient means for database quality control, called 'MisPred'. The work, recently published in the open access journal BMC Bioinformatics, was carried out as part of the EU project BioSapiens, supported with EUR 12 million in funding under the thematic area 'Life sciences, genomics and biotechnology for heath' of the Sixth Framework Programme (FP6). The MisPred tool, said the research team, uses five 'routines' for identifying suspect abnormal, incomplete or mispredicted entries based on the rationale that a sequence will probably be incorrect if some of its features conflict with the existing knowledge about protein-coding genes and proteins: (1) extracellular or transmembrane proteins must have appropriate secretory signals; (2) a transmembrane segment must be found on a protein with intra- and extra-cellular parts; (3) extracellular and nuclear domains must not occur in a single protein; (4) the number of amino acid residues in closely related members of a globular domain family must fall into a relatively narrow range; and (5) a protein must be encoded by exons located on a single chromosome. The team was led by Professor László Patthy, a researcher at the Institute of Enzymology of the Hungarian Academy of Sciences. 'Recent studies have shown that a significant proportion of eukaryotic genes are mispredicted at the transcript level,' said Professor Patthy. '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.' Professor Patthy pointed out, however, that a number of secreted proteins may actually 'lack secretory signal peptides because they are subject to leaderless protein secretion'. The Institute member added, '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 research showed that most mispredictions emerge due to the absence of expected signal peptides and violation of domain integrity. '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,' the team said. According to the team, the MisPred approach will give researchers more time to conduct more studies in erroneously identified genes.
Vifaa vipya vya kuboresha udhibiti wa ubora wa hifadhidata ya protini vinatokea: Hifadhidata za umma zinaendelea kuwa na jeni na protini zisizo za kawaida, zisizo kamili na zisizo na uhakika licha ya juhudi za hivi karibuni za kuboresha maelezo ya kompyuta ya genome. Makosa haya kuathiri vibaya kuegemea ya hifadhidata. "Lakini timu ya watafiti imeendelea kuwa na ""maelezo yasiyo ya kawaida, yasiyo kamili na yasiyo ya kawaida"" ya jeni na protini licha ya juhudi za hivi karibuni za kuboresha maelezo ya kompyuta ya genome." Makosa haya kuathiri vibaya kuegemea ya hifadhidata. Lakini timu ya watafiti imebuni chombo kipya kutoa njia ya ufanisi kwa ajili ya kudhibiti ubora wa database, aitwaye 'MisPred'. "Kama ilivyoelezwa katika jarida la ""Open Access Journal BMC Bioinformatics,"" utafiti huo ulifanyika katika mradi wa EU ""BioSapiens"" ambao unafadhiliwa na € 12 milioni katika eneo la ""Sayansi ya Maisha, Genome na Bioteknolojia kwa Afya"" ya Mpango wa Mfumo wa Sita wa EU." "Mifumo mitano ya ""misprinting"" hutumiwa kutambua viingilio visivyo vya kawaida, visivyo kamili au visivyo na uhakika kulingana na nadharia ya kwamba mfululizo wa viungo vya DNA huenda usiwe sahihi ikiwa baadhi ya sifa zake zinapingana na maarifa ya sasa kuhusu jeni na protini: (1) protini za nje ya seli lazima ziwe na ishara sahihi za secretory; (2) lazima sehemu ya ndani ya seli na ya nje ya seli ipate; (3) kikoa cha nje ya seli na nyuklia lazima visitokee katika protini moja; (4) idadi ya mabaki ya asidi ya amino katika familia ya kikoa ya globular lazima iwe katika safu ndogo." Utafiti huo uliongozwa na Profesa László Patthy, mtafiti katika Taasisi ya Enzymology ya Chuo cha Sayansi cha Hungaria. "Utafiti wa hivi karibuni umeonyesha kwamba sehemu kubwa ya jeni za eukaryotic hazitabiriwa vizuri katika kiwango cha maandishi", alisema Profesa Patthy. "Kwa kuwa utaratibu wa MisPred una uwezo wa kugundua makosa mengi, na inaweza kusaidia katika marekebisho yao, tunapendekeza kwamba inaweza kuboresha kwa kiasi kikubwa ubora wa data ya mfululizo wa protini kulingana na utabiri wa jeni. """ Hata hivyo, Profesa Patthy alionyesha kwamba huenda protini kadhaa zinazotenganishwa zikatoka kwa "peptidi za ishara za kutenganishwa kwa sababu zinatenganishwa na protini zisizo na kiongozi". Mwanachama wa Taasisi hiyo aliongeza, 'Vivyo hivyo, kwa sasa haiwezi kutengwa kwamba chimera za transchromosomal zinaweza kuundwa na zinaweza kuwa na kazi za kawaida za kisaikolojia. Hata hivyo, ukweli kwamba MisPred uchambuzi wa mfululizo wa protini ya Swiss-Prot database kutambuliwa wachache sana kama tofauti inaonyesha kwamba sheria ya MisPred ni kwa ujumla halali. Utafiti ulionyesha kwamba utabiri mbaya zaidi hutokea kwa sababu ya kutokuwepo kwa peptidi za ishara zinazotarajiwa na ukiukaji wa uadilifu wa kikoa. "Kwa kuvutia, hata seti ya data ya UniProtKB au Swiss-Prot iliyopangwa kwa mkono imechafuliwa na protini zisizo za kawaida, ingawa kwa kiwango kidogo kuliko UniProtKB au Trimble au viingilio vya Ensemble au GNOMO.""" Kulingana na timu hiyo, mbinu ya MisPred itawapa watafiti muda zaidi wa kufanya masomo zaidi katika jeni zilizotambuliwa kimakosa.