Gene Finders, DNA, Protein Coding Genes, Open Reading Frames, Signal Sensors, Codons, Polyadenylation Sites

Scholarships Dictionary Visa Details Study Abroad Exam Results Online Test Jobs

	Home
Bioinformatics and Data Mining - In Silico Biology Bioinformatics and Data Mining - In Silico Biology - Introduction History of Bioinformatics List of Major Events in Bioinformatics Web Services as Bioinformatics Tools Alignment Tools Some Important Web Sites Commonly Used For Bioinformatics The FASTA Family PatMatch Blast - Earlier Versions Blast - Later Versions ParAlign ProteinEngine and Transeq Interpro Multiple Sequence Alignment Tools Clustalw Phylip BioNumeric Version Multipurpose Analysis Tool / Biotechnix 3D Designing of PCR Primers Tools for In Silico Discovery of SNPs Tools for In Silico Mining of SSRs Assembly Packages for Large Scale Genome Sequencing

Home >> Biotechnology and Genomics >> Bioinformatics and Data Mining - In Silico Biology >> Gene Finders

Your Ad Here	Gene finders Once a large amount of DNA has been sequenced, the major task is to understand and detect in these unannotated sequences (it) the protein coding genes, (ii) the structure of these genes (demarcation of control regions, exons, introns and untranslated regions, the UTRs) and (iii) the location of repetitive sequences and their nature. The gene finders are the programmes that identify all open reading frames (ORFs) in unannotated DNA. They use a variety of approaches to locate genes. The major methods for identification of genes can be divided into two types: (i) Signal sensors are the methods that identify the presence of genes by detecting local sites such as start and stop codons, branchpoints, splice sites, promoters and terminators of transcription, polyadenylation sites and ribosomal binding sites. (ii) content sensors are the methods that identify the genes through the use of nucleotide frequencies (relative proportions of GC and AT base pairs) and dependency that help in differentiating coding and non-coding sequences. For instance, coding regions of DNA sequences have a strong three base periodicity, which the non-coding sequences would lack
Most of the gene finding tools at present combine both the signal and the content sensors to identify complete gene structure. Some commonly used programmes for gene finding include GRAIL, GENSCAN, PROCRUSTES, GENEWISE, GENESCAN, PROCRUSTES, SANGER Centre Genefinder and GlimmerM/R (GlimmerM/R is specialized for Arabidopsis and rice, etc)
Known gene in database Names of genes with their sequences in the database are also available. Unfortunately, some genes have multiple names, and unrelated genes may also often share a common name. Therefore, gene names are providing a hindrance, rather than a help in finding the closest relative of a gene. In view of this, attempts are being made to impose standard names across the board. These efforts are meeting stiff resistance, and approaches that would give unique ID numbers to genes seem unlikely to take off, unless journals enforce the system. But a coalition of leading geneticists may have the answer. The Gene Ontology (GO) Consortium is sidestepping the naming issue by developing software to scan the genomic database and link related genes to one another by using the names, which consistently describe their function, regardless to what the genes are called	Your Ad Here
Program cpglot This program released in September 2001 is available on EMBOSS home page and plots CpG rich areas. CpG refers to a cytosine (C) residue immediately followed by a guanine (G) in the genomic sequences and a region rich in CpG island. These CpG islands are resistant to methylation and tend to be associated with genes which are frequently switched on. Frequencies of CpG islands have also been used for predicting the number of genes in a genome and for several other purpose including taxonomic clustering

	Home
Demiglace EST Clustering Packages Gene Finders Central Repository Biological Literature / PubMed Bioinformatics Instiutes and Databases / Databanks Bioinformatics Institutes - NCBI, EBI, SIB National Centre for Biotechnology Information - NCBI European Bioinformatics Institute EBI Bioinformatics Center kyoto University Swiss Institute of Bioinformatics - SIB The Databases / Data Banks Swiss-Prot, Prosite and ExPAsy GenBank, Flybase, DDBJ RefSeq Bioinformatics Training at ICGEB Training in Universities Bioinformatics Market Data Mining Selected Companies and Their Areas of Interest in the Field of Bioinformatics Limitations of Bioinformatics and Data Mining

Language >> English | Français | Español | Deutsch | Italiano | Portugues | Japanese | Korean | Sim-Chinese