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Comparative Genomics - Bioinformatics Komparativna genomika - bioinformatiku

Comparative Genomics Introduction Komparativna genomika Uvod

Comparative genomics is the study of relationships between the genomes of different species or strains. Komparativna genomika je proučavanje odnosa između genoma različitih vrsta ili naprezanja. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary processes that act on genomes. Komparativna genomika je pokušaj iskoristiti informacije koje se potpisi izbor razumjeti funkciju i evolucijski procesi koji djelovati na genocid. While it is still a young field, it holds great promise to yield insights into many aspects of the evolution of modern species. Dok je još mlada polju, ona posjeduje veliku obećanje da prinosa uvide u mnogim aspektima evoluciji modernih vrsta. The sheer amount of information contained in modern genomes (several gigabytes in the case of humans) necessitates that the methods of comparative genomics are mostly computational in nature. Strmim količinu informacija koje su sadržane u modernom genoma (nekoliko gigabajta u slučaju čovječji) necessitates da je metoda komparativne genomike su uglavnom računalna u prirodi. Gene finding is an important application of comparative genomics, as is discovery of new, non-coding functional elements of the genome. Pronalaženje gena je važno primjena komparativna genomika, kao što je otkriće novih, ne-kodiranje funkcionalnih elemenata u genom.

Comparative genomics exploits both similarities and differences in the proteins, RNA, and regulatory regions of different organisms to infer how selection has acted upon these elements. Komparativna genomika eksploatira i sličnosti i razlike u proteina, RNA i regulatorne regije različitih organizama na zaključak kako se ponaša na izbor ovih elemenata. Those elements that are responsible for similarities between different species should be conserved through time (stabilizing selection), while those elements responsible for differences among species should be divergent (positive selection). Onih elemenata koji su odgovorni za sličnosti između različitih vrsta bi trebala biti sačuvano kroz vrijeme (stabilizirajuce selekcija), dok su one elementi odgovorni za razlike među vrsta bi trebala biti divergent (pozitivna selekcija). Finally, those elements that are unimportant to the evolutionary success of the organism will be unconserved (selection is neutral). Konačno, one elemente koji su važno da se evolucijski uspjeh u organizam će biti unconserved (izbor je neutralan).

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is one of the important goals of the field. Identificiranje mehanizme eukaryotic genom evolution by komparativna genomika je jedan od važnih ciljeva u polju. It is however often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. To je međutim često komplicirano je mnogobrojnost događaja koji su se dogodili tijekom povijesti pojedinih lineages, ostavljajući samo iskrivljene i superimposed tragovi u genom svakog živoga organizma. For this reason comparative genomics studies of small model organisms (for example yeast) are of great importance to advance our understanding of general mechanisms of evolution. Iz tog razloga komparativna genomika studije malih model organizmi (npr. kvasac) su od velike važnosti da se unaprijed naše razumijevanje općih mehanizama evolucije.

Having come a long way from its initial use of finding functional proteins, comparative genomics is now concentrating on finding regulatory regions and siRNA molecules. Nakon što dođe dug put od prvobitnog korištenje pronalaženje funkcionalne bjelančevine, komparativna genomika je sada koncentriraju na pronalaženje regulatorne regije i siRNA molekula. Recently, it has been discovered that distantly related species often share long conserved stretches of DNA that do not appear to code for any protein. Nedavno je otkriveno da distantly srodne vrste često dijele dugo sačuvano proteže od DNA koje se ne pojavljuju se kod za bilo koji protein. It is unknown at this time what function such ultra-conserved regions serve. To je u ovom trenutku nepoznata funkcija kao što ultra-konzervirani regije služiti.

Computational approaches to genome comparison have recently become a common research topic in computer science. Računski pristupe genom usporedbi nedavno postala zajednička istraživanja topic in Računalna znanost. The development of computer-assisted mathematics (using products such as Mathematica or Matlab) has helped engineers, mathematicians and computer scientists to start operating in this domain, and a public collection of case studies and demonstrations is growing, ranging from whole genome comparisons to gene expression analysis. Razvoj računalno potpomognuto matematike (koristeći proizvode kao što su Mathematica ili Matlab) je pomogla inženjeri, mathematicians i računalo da biste pokrenuli znanstvenika koji rade u ovom domenu, kao i javnih kolekcija case studies i demonstracija raste, u rasponu od čitav genom usporedbe na gene izraz analiza. This has increased the introduction of different ideas, including concepts from systems and control, information theory, strings analysis and data mining. Time je povećana uvođenje različitim idejama, konceptima iz sustava, uključujući i kontrolu, teorija informacija, analiza stringova i data mining. It is anticipated that computational approaches will become and remain a standard topic for research and teaching, while students fluent in both topics start being formed in the multiple courses created in the past few years. To je računalna predviđa da će se pristupi i dalje standardni topic za istraživanja i nastave, a studenti tečno u obje teme početi se formirala u više tečajeva izrađenih u posljednjih nekoliko godina.

Evolutionary Conserved Region Bioinformatics Evolucijski sačuvanih Regija bioinformatiku

Evolutionary Conserved Regions also called ECRs for short are regions of sequence (usually DNA) that have been mapped to align with other genomes and are conserved. Evolucijski sačuvanih Regije i pozvao ECRs za kratko su regije slijed (obično DNA) koji su bili mapirani uskladiti s drugim genocid i konzervirani.

ECRs within alignments of the genomes are presented in this graphical browser, which depicts and color-codes ECRs in relation to known genes that have been annotated in the base genome. ECRs unutar alignments od genoma su izneseni u ovom grafički preglednik, koji prikazuje i boja-kodovi ECRs u odnosu na poznati geni koji su povezani u osnovni genom. 'Grab ECR' feature allows users to rapidly extract sequences that correspond to any ECR, to visualize underlying sequence alignments and/or identify conserved transcription factor binding sites. 'Zgrabite ECR' značajka omogućuje korisnicima da brzo izvuci sekvence koji odgovaraju bilo kojem ECR, zamišljati da je ispod sequence alignments i / ili identifikaciju konzervirani transkripcije factor binding sučelja.

ECR Browser is a new dynamic whole-genome navigation tool for the visualization and study of evolutionary relationships between vertebrates and non-vertebrate genomes. ECR Browser je novi dinamički cijeli genom-navigacijski alat za vizualizaciju i studija evolucijski odnos između kralješnjaka i ne-kralježnjaci genocid. ECR Browser is constantly being updated to include the most recently available sequenced genomes (currently: human, dog, mouse, rat, chicken, frog two pufferfish (Fugu and Tetraodon), zebrafish, and 6 fruitflies). ECR Browser je stalno ažuriraju se uključiti u posljednje vrijeme dostupne poredan genoma (trenutno: ljudskih, pas, miš, štakor, pileći, žaba dva pufferfish (Fugu i Tetraodon), zebrafish, i 6 fruitflies). Ovcharenko, MA Nobrega, GG Loots, and L. Stubbs ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes Nucleic Acids Research, 32, W280-W286 (2004) Ovcharenko, MA Nobrega, GG Loots, L. i Ada Lukacka ECR Browser: alat za visualizing i pristupaju podacima iz usporedbe više kralježnjaci genocid Nucleic Acids Research, 32, W280-W286 (2004)

ECRbase is the Database of Evolutionary Conserved Regions (ECRs), Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes created using ECR Browser alignments ECRbase je baza podataka evolucijski sačuvanih Regije (ECRs), promotori, i Transkripcija Factor Binding stranice u Kralježnjaci genocid kreirana koristeći ECR Browser alignments

Bioinformatics Forum Bioinformatika Forum

Discuss and post questions about protein expression in the Bioinformatics Forum . Diskusiji i postavljati pitanja u vezi proteina izražavanja u bioinformatiku Forum.