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Učinkovito kodiranje zaporedij DNA
Murovec, Boštjan (Author), Stres, Blaž (Author)

URLURL - Presentation file, Visit http://www.dlib.si/details/URN:NBN:SI:doc-7WWR7RSM This link opens in a new window

Abstract
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 (r6)
Tipology:1.01 - Original Scientific Article
Organization:BF - Biotechnical Faculty
Year:2008
Publisher:Biotehniška fakulteta
Number of pages:str. 151-162
Numbering:Letn. 92, št. 2
UDC:575
ISSN on article:1581-9175
COBISS.SI-ID:2412168 Link is opened in a new window
Views:470
Downloads:65
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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 This link opens in a new window

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

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