BOL

Hi Govardhan,

If the protein or nucleotide sequences are known then you can use BLAST. It is better to perform searches at the protein level, either with translations of the nucleotide sequences or by direct protein-protein BLAST. This is because of the degeneracy of the genetic code, the greater information available in amino acid sequence, and the more sophisticated algorithm in protein-protein BLAST.

If any nucleotide sequence pattern are know then you can use this script http://bioinformaticsonline.com/file/view/4882/detect-the-sequence-pattern-and-its-location-in-fasta-file-with-match-and-mismatches-information to find them in genome. 

Thanks

Hi Govardhan,

I guess from above mentioned genome size that you are working on prokaryotes genome and looking for a tool to predict the origin and terminus of replication. I hope following tool will be helpful for your research.

Oriloc: http://bioinformatics.oxfordjournals.org/content/16/6/560.long

http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/oriloc.html

Oriscan: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC395781/

Ori-Finder: http://www.biomedcentral.com/1471-2105/9/79

For futher reading :

http://genomebiology.com/content/13/4/R27

http://bib.oxfordjournals.org/content/9/5/376.full

Best of luck for your research.

Thanks