Gene Finding
... Detecting ORF Simple Idea: If there is no gene encoded then the expected frequency of STOP codon is 3/64 codons ORF – open reading frame, a sequence of codons with no STOP codon Simple Algorithm: 1. scan until you find a stop condon, in all reading frames. 2. Scan back to find a start codon. 3. ...
... Detecting ORF Simple Idea: If there is no gene encoded then the expected frequency of STOP codon is 3/64 codons ORF – open reading frame, a sequence of codons with no STOP codon Simple Algorithm: 1. scan until you find a stop condon, in all reading frames. 2. Scan back to find a start codon. 3. ...
Project guidelines: 1. Literature review 2. Learn and run two existing
... Motif finding. Take a group of related proteins and find motifs. Do they match the reported motifs? Why or why not? Might there be other, unreported motifs? What assumptions are made by available motif-finding programs? Gene finding. Choose a fairly large genome contig from any organism. Predict whe ...
... Motif finding. Take a group of related proteins and find motifs. Do they match the reported motifs? Why or why not? Might there be other, unreported motifs? What assumptions are made by available motif-finding programs? Gene finding. Choose a fairly large genome contig from any organism. Predict whe ...
Principles of genetic engineering
... Genetic engineering, also known as recombinant DNA technology, means altering the genes in a living organism to produce a new genotype. Various kinds of genetic modification are possible: – inserting a foreign gene from one species into another – altering an existing gene so that its product is chan ...
... Genetic engineering, also known as recombinant DNA technology, means altering the genes in a living organism to produce a new genotype. Various kinds of genetic modification are possible: – inserting a foreign gene from one species into another – altering an existing gene so that its product is chan ...
Gene prediction
In computational biology gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced.In its earliest days, ""gene finding"" was based on painstaking experimentation on living cells and organisms. Statistical analysis of the rates of homologous recombination of several different genes could determine their order on a certain chromosome, and information from many such experiments could be combined to create a genetic map specifying the rough location of known genes relative to each other. Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, gene finding has been redefined as a largely computational problem.Determining that a sequence is functional should be distinguished from determining the function of the gene or its product. Predicting the function of a gene and confirming that the gene prediction is accurate still demands in vivo experimentation through gene knockout and other assays, although frontiers of bioinformatics research are making it increasingly possible to predict the function of a gene based on its sequence alone.Gene prediction is one of the key steps in Genome annotation, following Sequence assembly, the filtering of non-coding regions and repeat masking.Gene prediction is closely related to the so called 'target search problem' investigating how DNA-binding proteins (transcription factors) locate specific binding sites within the genome. Many aspects of structural gene prediction are based on current understanding of underlying biochemical processes in the cell such as gene transcription, translation, protein–protein interactions and regulation processes, which are subject of active research in the various Omics fields such as Transcriptomics, Proteomics, Metabolomics, and more generally structural and functional genomics.