20.500.12556/RUL-109586 Primerjava bioinformacijskih orodij za de-novo in z genomom vodeno sestavljanje prepisanih genov Comparison of bioinformatic tools for de-novo and genome guided transcript assembly V dobi hitrega napredka orodij za sekvenciranje nove generacije so bioinformatska orodja za obdelavo velike količine podatkov, ki ob tem nastane izrednega pomena. V zadnjih letih se vedno bolj uveljavlja metoda RNA-seq za raziskave v transkriptomiki. Pri tem nastanejo kratki odčitki, ki pa jih je potrebno v nadaljevanju sestaviti v najbolj verjetno obliko prepisanega gena. Pri sestavljanju prepisanih genov poznamo dva pristopa. Prvi je z genomom vodeno sestavljanje prepisanih genov, pri čemer odčitke poravnamo z referenčnim genomom. Drugi pristop pa je sestavljanje prepisanih genov de-novo, pri katerem odčitke sestavljamo brez referenčne matrice. Oba pristopa imata tako prednosti kot slabosti. Z genomom vodeno sestavljanje je primerno za sestavljanje prepisanih genov modelnih organizmov. Pri teh so genomi dobro anotirani in jih lahko uporabimo kot referenco za poravnavo odčitkov. Pristop de-novo pa je bolj primeren za organizme katerih genomov ne poznamo, še niso sekvencirani. Namen tega diplomskega dela je predstavitev obeh pristopov, pregled nekaterih orodij ter primerjava le teh. In the age of fast development of tools for next-generation sequencing, the bioinformatics tools for processing of a large amount of data have an exceptional meaning. In the last few years, the RNA-seq method has established itself as a useful method in transcriptomics. Its output are short reads, which ha to be assembled in a possible transcripts. For transcript assembly two approaches are available. The first one is genome-guided assembly of transcripts. Using this approach the RNA-seq reads are aligned to the reference genome. The second approach is de-novo transcript assembly where we do not have the reference sequence, so the transcript is built from scratch. Both approaches have pros and cons. Genome guided assembly is appropriate for model organisms since their genomes are well annotated and used as a reference. De-novo approach is more appropriate for non-model organisms where genome sequence is not available. The purpose of this work is the presentation of both approaches, review of some commonly used tools and their comparison. bioinformatika bioinformacijska orodja transkriptomika sekvenciranje genom bioinformatics bioinformatic tools transcriptomics sequencing genome true false false [P. Jelovšek] Slovenski jezik Angleški jezik Diplomsko delo/naloga 2019-09-06 07:45:15 2019-09-06 07:45:17 2022-08-21 03:43:07 0000-00-00 00:00:00 2019 0 0 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 601.4:575.116.4:577.212.3:575.112:004(043.2) 167390 9366137 7734.pdf 7734.pdf 1 74054B95DD027C0AB7166D33ED5A885F 7078ec9821609284dbe79a3f516a1bf1f0d548d279b8ec7dd002ebc5f310d5b0 e7302a33-a1b6-11eb-a523-00155dcfd717 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=121167 Biotehniška fakulteta 0 0 0