I got the sequence from the database in the FASTA format. I need to find the CDS region from the same. The sequence is from KEGG pathway database.
For all the entries that I have seen at KEGG database, they already report the CDS in the section NT seq (from atg to stop codon), along with the corresponding translated protein. Are you sure that is not the case for your gene of interest?
If not, you would need to find all possible ORFs in your sequence and get the one that corresponds to the reported protein (usually the largest ORF found). You could try this online tool for that: http://www.ncbi.nlm.nih.gov/projects/gorf/
Its not straight forward, I guess. If it is from well sequenced organism, then it is probably easy. If the reference file or gene information file is not available, then you might have to predict the ORFs in the Fasta sequence to find CDS.
For all the entries that I have seen at KEGG database, they already report the CDS in the section NT seq (from atg to stop codon), along with the corresponding translated protein. Are you sure that is not the case for your gene of interest?
If not, you would need to find all possible ORFs in your sequence and get the one that corresponds to the reported protein (usually the largest ORF found). You could try this online tool for that: http://www.ncbi.nlm.nih.gov/projects/gorf/
you can use blastX from "http://blast.ncbi.nlm.nih.gov/Blast.cgi" to find out the possible ORF in comparison to other well known proteins.
yup go for ORF and the largest one will used for further protein analysis
You can use "ESTScan" to predict the CDS, it can handle Frameshifts. If you have a close homolog for your protein of interest you can use the homolog protein as reference to predict the CDS of the target dna using FrameBot. It corrects frameshifts too.Use the "GLOCAL" model, if the DNA is supposed to be of full length (http://sourceforge.net/projects/rdpframebot/)
If you work on a relatively well-sequenced organism, you can try a gene prediction tools such as GeneMark (http://opal.biology.gatech.edu/) and use in combination with ESTScan and Blastx. Once you have a good prediction, you can simply amplify the cDNA, then clone and sequence it to confirm your gene structure.
http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
try this specialized blast type to directly get CDS for ur protein or nucleotide seq
you could use the RAST annotation tool.
ORF finder from NCBI has sequence limit till 50kb.
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