Outline

∗ Gene prediction

∗ Gene Tools 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 Tools

• Gene Tools is a web-service providing access to a database that brings together information from a broad range of resources

• It’s the part where use of gene tools becomes neccessary Gene Tools

• The basic online tools used are 1. GenScan 2. Glimmer 3. GeneID Other tools Gene Tools

Genscan 1. GENSCAN is an program to identify complete gene structures in genomic DNA.

2. Can be used to predict the location of genes and their exon‐intron boundaries in genomic sequences from a variety of organisms. Gene Tools

∗ Genscan Homepage Gene Tools

∗ Upload the DNA sequence in fasta format

∗ Then click RUNGENSCAN The output of the DNA sequence is given on right hand side : Glimmer

∗ Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.(Gene Locator and Interpolated Markov Modeller)

∗ Glimmer is the system of choice for genome annotation efforts on a wide range of bacteria, archaeal, and viral species due to high accuracy. Gene Tools

∗ Glimmer was used by the DNA Databank of Japan (DDBJ) to re-annotate all bacterial genomes in the International Nucleotide Sequence Databases.

∗ It is also being used by this group to annotate viruses The home Page of Glimmer We have to Paste the Sequence in fasta format

Then we will Run Glimmer RESULT OF GLIMMER

∗ The output is shown below Gene Tools

∗ GeneID homepage Gene Tools

GeneID 1. Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. 2. General Steps a) In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs) Gene Tools

b) In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. c) Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons Gene Tools

∗ The input sequence is nucleotide ∗ We also give GFF format or so called General feature Format ∗ Finally click the button submit Gene Tools

∗ The final output is shown in right hand side Gene Tools

∗ Other tools 1. Poly-A site prediction HCpolyA is used for Poly A Site prediction using Hammering clustering method. 2. Exon Prediction: ORF finder graphical analysis tool that finds all open reading frames of selectable minimum size of a user’s sequence example Genefinder Gene Tools

3. tRNA gene prediction: tRNA scan is used for genomic tRNA Gene Tools

Tools Predictio Sen Spe Sensiti Specifi Missed n sitiv cifi vity city Exon ity city exon exon FGENES Gene 83 93 73 78 15 structure GENEId Gene 69 77 42 46 28 structure GENE Gene 66 79 35 40 29 PARSER Structure GENSCAN Gene 93 93 78 81 9 Structure GRAIL II Gene 83 87 ‐‐‐‐ 52 25 Structure MIZEF Gene 87 95 78 86 14 Structure References

∗ http://genome.crg.es/software/geneid/ ∗ http://genes.mit.edu/GENSCANinfo.html ∗ http://en.wikipedia.org/wiki/GLIMMER ∗ http://www.ncbi.nlm.nih.gov/genomes/MICROBES/gli mmer_3.cgi ∗ Bioinformatics Methods and Application by S.C. Rastogi THANK YOU