cpDNAdb

DNA comparisons 

cpDNAdb can be run in one personal computer / workstation - it doesn't need a supercomputer nor a framework of several PCs (as eg. CODIS). Below is listed test results, which were run in one PC (CPU: 3.4 GHz, RAM: 2 GB). cpDNAdb handled millions of identifiers in less than 4 minutes, which is much faster than the comparison that has been made between German's and Austria's DNA databases.

A new search / comparison algorithm is used in cpDNAdb and that makes it possible to complete the ( fastest ?) STR comparison with set allowed microallele and loci differences.

Results of the latest program version (2013):

• example database d20M.txt : 20 millions identifiers, each with 16 loci and each locus with 2 alleles.
• Comparison of N vs N in d20M.txt:
• comparison with 0 allowed difference : comparison time 209 seconds
• comparison with 2 allowed differences and 2 microallele difference: comparison time 40 min
• More results : Results 2013
• Download demo program : cpDNAdemo
• Download test data for cpDNAdemo: d1M.zip

Results of the previous program version (2009):

• example database u50M.txt : 50 millions identifiers, each with 16 loci and each locus with 2 alleles.
• Comparison of N vs N in u50M.txt:
• comparison with 1 allowed difference : comparison time 711 seconds
• comparison with 2 allowed differences : comparison time 1795 seconds = 30 min

Results of previous program version (2007):

• example database 1 : DB_452000
• example database 2 : DB_852000
• Comparison of DB1 and DB2 :
• Results of comparison with 1 allowed difference : Res-file (comparison time 12 seconds)
• Results of comparison with 2 allowed differences : Res-file (comparison time 46 seconds)

• example database 3 : DB_2000000
• example database 4 : DB_4000000
• Comparison of DB3 and DB4 :
• Results of comparison with 1 allowed difference : Res-file (comparison time 59 seconds) (file size 9 MB)
• Results of comparison with 2 allowed differences : Res-file (comparison time 231 seconds) (html file as zip)

Large DNA Databases already exists in many European countries [DNA databases in Europe]. To find all the possible hits between those databases, a mass comparison of data is needed at least in the beginning of data exchange. A mass comparison should be done also in a case of changes to data requirements (e.g. adaption of new DNA loci) or to match requirements. cpDNAdb makes it possible whenever such comparison is needed.

Licences available :

• 100 000 eur : 2 licences / year / workstation
• 1 Meur : 50 licences / year / workstation

REFERENCES

• Some related details (mainly links to Finnish pages, e.g. the Parliament of Finland)

• Agreement on a pan-European network of police databases for more effective crime control 15.02.2007
• "For example, under the treaty Austria and Germany have been able to check the contents of their national DNA (forensic) databases against each other since early December 2006. This is the first time that two countries have granted each other access to their national police databases using a hit/no hit procedure."
• "In the first eight weeks alone, German data enquiries resulted in 1,500 matches in the Austrian database, while Austrian enquiries led to 1,400 matches in the German database, including 32 matches related to homicides."
• EU Informal Meeting 14.01.2007 Results of the automated comparison of DNA profiles in the German and Austrian national DNA databases
• Genotype Profiles from FBI 01.07.1999
• Other DNA identifier algorithms Comparing identification methods for DNA investigations of crimes and accidents, authors: Jukka Ollikainen, M.Juhola (University of Tampere :n yliopisto))
• Prümin sopimus läpi suuressa valiokunnassa äänestysten jälkeen 21.6.2006
• Prümin sopimuksen täytäntöönpanoa koskeva sopimus ja yhteinen poliittinen julistus allekirjoitettiin 05.12.2006
• Eduskunta hyväksyi täysistunnossa Prümin sopimuksen äänin 148-31. 13.2.2007 (Parliament accepted Prüm agreement)
• Poliisin tietokannat seitsemässä maassa 22.1.2007 Suomen dna- ja sormenjälkirekisterit avautuvat
• Helsinki , Sisäasiainministeriö: Prümin sopimus 17.02.2006
• "DNA-tietojen vertailu on sopimuksen mukaan tarkoitus toteuttaa viitetietojärjestelmän avulla. Tämä koskee sekä varsinaisia DNA-tunnisteita että tahratunnisteita eli rikospaikalle jääneistä tahroista tehtyjä DNA-tunnisteita."
• "Suomen näkemyksen mukaan tarkoituksenmukaisin tapa vertailla DNA-tietoja keskenään olisi tehdä sellaiset tekniset muutokset kunkin sopimusvaltion järjestelmiin, että järjestelmät kykenisivät automaattisesti vertailemaan talletettuja numeerisia tietoja ja ilmoittamaan osumista."
• "Ajamalla tietoja ristiin voitaisiin saada useita osumia, mikä voisi auttaa selvittämättä jääneiden (”pimeiden”) rikosten selvittämisessä."
• Prümin sopimus - DNA-rekisterit auttaneet kuukaudessa jo yli 3000 rikoksen selvittämistä 16.1.2007
• EUROOPAN UNIONIN NEUVOSTO: lehdistötiedote 15.02.2007
• Saksan ja Itävallan tietojen vertailu
• ”osuma/ei-osuma”-haku muutamassa minuutissa
• Sisäasiainministeriö: E-JATKOKIRJELMÄ 22.01.2007
• cpDNAdb is one implementation of a new fast algorithm. Now it solves the N <==> N -comparison problem of DNA identifiers. It is under study, to which other difficult problems and Big Data cases it can be used. Two areas are under study: a) counter-terrorism and surveillance data and b) companies' production(matter-to-product) and product-to-market-customerbehaviour data. Link to be defined.
c) network routes and TSP solutions by JuOL Oulu - Kuusankoski - Kouvola - Kotka - Lahti - Helsinki - Tampere:)

Last update: 13.11.2022