Učinkovito kodiranje zaporedij DNA

Murovec, Boštjan (author), Stres, Blaž (author)

V zadnjem obdobju smo priča znatnemu naraščanju uporabe mikroračunalnikov pri raziskavah in analizah zaporedij DNA. Molekule DNA so računalnikom najpogosteje predstavljene v obliki zapisov v formatu FASTA , ki kodirajo sekvence DNA v obliki ASCII niza štirih nukleotidnih oznak A, G, C in T, katerim se po potrebi pridružijo še degenerativne kode in znak za presledek, ko gre za množice med seboj poravnanih zaporedij DNA. Zapis FASTA je dojemljiv za biologa in enostaven za programerja, ki razvija računalniški program, saj si pri razvoju lahko pomaga z bogatim naborom obstoječih knjinic za delo z znakovnimi polji. Kljub omenjenim prednostim ima zapis FASTA določene slabosti, kot je manj učinkovito iskanje zaporedij nukleotidov, še posebej ob prisotnosti degenerativnih kod. Druga slabost izvira iz dejstva, da vsak posamezni znak FASTA za presledek zasede po en zlog računalniškega pomnilnika,kar je ob prisotnosti velikega števila presledkov neučinkovito in tudi dodatno manjša hitrost iskanja nukleotidnih zaporedij. Zaradi omenjenih slabosti predstavljamo alternativni zapis zaporedij DNA, ki omogoča hitrejše iskanje nukleotidnih zaporedij in učinkovitejše shranjevanje informacij o poravnavi, kar vodi v hitrejše delovanje programov in odpira monost shranjevanja večjega števila zapisov DNA v delovni pomnilnik računalnika.

• Language: Slovenian
• Keywords: molekulkarna genetika, bioinformatika DNK, kodiranje zaporedij
• Work type: Not categorized
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publisher: Biotehniška fakulteta
• Year: 2008
• Number of pages: Str. 151-162
• Numbering: Letn. 92, št. 2
• PID: 20.500.12556/RUL-57733
• UDC: 575
• ISSN on article: 1581-9175
• COBISS.SI-ID: 2412168
• Publication date in RUL: 10.07.2015

MUROVEC, Boštjan and STRES, Blaž, 2008, Učinkovito kodiranje zaporedij DNA. Acta agriculturae Slovenica [online]. 2008. Vol. 92, no. 2, p. 151–162. [Accessed 13 April 2025]. Retrieved from: http://www.dlib.si/details/URN:NBN:SI:doc-7WWR7RSM

Record is a part of a journal

• Title: Acta agriculturae Slovenica
• Shortened title: Acta agric. Slov.
• Publisher: Biotehniška fakulteta
• ISSN: 1581-9175
• COBISS.SI-ID: 213840640

Secondary language

• Language: English
• Title: Efficient coding of DNA

Abstract

Microcomputers have become ubiquitous tools for DNA research and analysis. Before DNA sequences can be fed into computer programs they need to be suitably coded, which is usually done in a widely accepted FASTA format. According to this scheme, DNA sequence is represented as an ASCII string of four nucleotide characters A, G, C and T, possibly extended with additional codes for representation of degenerated sites, and a character code for FASTA blanks when dealing with aligned DNA sequences. FASTA representation is intuitive for biologists and it eases development of programs since developer scan utilize a myriad of available libraries for working with ASCII strings. Despite the mentioned advantages, FASTA format possesses certain drawbacks like inefficient searching for substrings, especially in the presence of degenerative codes. The second disadvantage is inefficient storage of FASTA blank characters, since each such character occupies one byte of memory. Substring searching speed is also negatively affected in the case of excessive number of blanks. Due to the stated drawbacks, we propose an alternative coding of DNA sequences, which enables faster searching of substrings and efficient storage of FASTA blanks, with the result that a greater set of DNA sequences can be held in working memory of a computer and processed faster.

• Keywords: molecular genetics, bioinformatics, DNA sequences, coding