27 May 2011

GENE PREDICTION TOOL-GENSCAN


AIM
                        To predict the gene regions in the given genomic DNA sequence by using a gene prediction tool like genscan.

INTRODUCTION
Genscan server is maintained at MIT provides access to the program genscan for predicting the locations exons and introns structures in genomic sequences from a variety of organisms. The server can accept sequences upto one million base pairs in length. The accuracy of genscanis somewhat sensitive to exon length. Genscan is by far the most comprehensive and sophistication gene prediction tool available for free.

EXPLAINATION
(1) GN.Ex---It indicates gene number, exon number.
(2) INIT---Initial Exon
(3)INTR---Internal Exon
(4)TERN---Terminal Exon
(5)SNGL---Single Exon Gene
(6)PROM---Promoter
(7)PLYA---Poly A Signal
(8)S---DNA strand (+indicates input strand ) (-ve indicates complementary strand)
(9)BEGIN---Beginning position of Exon
(10) END---Ending position of Exon
(11)LEN---Length of Exon
(12)FR--- It indicated Reading Frame
(13)PH--- Net phase of Exon
(14)I-AC--- Initiation signal
(15)DO-T--- Terminal signal score
(16)COD-RG--- Coding region score
(17)P--- Probability of Exons
(18)TSE-R--- Exon’s score {depends on length}

SCORE
             The score of a predicted feature exon are splice side is a log-odds measure of the quality of a feature based on local sequence properties.

PROBABILITY
                 The probability of a predicted exon is the estimated probability under genscan’s model. Genomic sequence structure that the exon is correct.

PROCEDURE
                 We can utilize the file transfer protocol feature of NCBI to obtain complete genome sequences of any of the sequenced organisms freely available. To do this we enter the ftp site of NCBI. It is available at

                                                   www.ncbi.nlm.nih.gov/ftp

                   We access the genome directories of all available. A list of organisms
(1)  We enter the ftp site of NCBI.
(2)  From this site we retrieve the complete genome sequence of any organism.
                    (3) We enter into the genscan server at

                                                   http://genes.mit.edu/GENSCAN.html

                    (4) We upload the retrieved genomic sequence and run Genscan.

                    (5) Thus the predicted exons were analysed.




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