Parametrizirani odabir srodnih proteinskih sljedova u svrhu procjene starosti gena

master's thesis

• Title (english): Parametrized selection of related protein sequences required for the estimation of gene age
• Author: Antea Ribarić
• Mentor: Mirjana Domazet-Lošo (mentor)
• Committee member: Mirjana Domazet-Lošo (predsjednik povjerenstva)
• Committee member: Tomislav Jagušt (član povjerenstva)
• Committee member: Danijel Mlinarić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2023-07-03, Croatia

Abstract

U ovom radu je provedena filostratigrafska analiza kako bi se odredila starost gena
Homo sapiensa u usporedbi s drugim eukariotskim organizmima. Kao temelj filostratigrafije korišteni su bioinformatički alati MMseqs2 i BLAST za pretragu sličnosti
gena. Analizirano je kretanje starosti gena s obzirom na graničnu E-vrijednost te je
dodan novi uvjet za određivanje statističkog značaja pogodaka, dinamički prag lažne
homologije. Sklonost lažnoj homologiji je procijenjena pretragom sličnosti nad reverznom ciljnom bazom. Rezultati su pokazali da je alat BLAST skloniji lažnoj homologiji
u usporedbi s alatom MMseqs2, a određene starosti gena su se pokazale kao robusne i
nisu značajno ovisile o odabiru granične E-vrijednosti.

Abstract (english)

In this paper, a phylostratigraphic analysis was implemented to determine the age
of Homo sapiens genes in comparison with other eukaryotic organisms. Bioinformatics tools MMseqs2 and BLAST were used as the basis of phylostratigraphy to search
for gene similarity. The age distribution of genes was analysed with regard to the
E-value threshold, and a new criterion was added for determining the statistical significance of hits, the dynamic threshold of false homology. The propensity for false
homology was assessed by a similarity search over the reverse target base. The results
showed that BLAST is more prone to false homology compared to the MMseqs2, and
estimated gene ages were shown to be robust and not significantly dependent on the
choice of E-value cut-off.

• Keywords: starost gena; filostratigrafija; MMseqs2; BLAST; lažna homologija; E-vrijednost
• Keywords (english): gene age; phylostratigraphy; MMseqs2; BLAST; false homology; E-value
• Language: croatian
• URN:NBN: urn:nbn:hr:168:451749
• Study programme: Title: Computing; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2023-10-11 10:20:38