Using 'Highlight sequence features' option in NCBI, we have retrieved all CDS of a full genome. From this data set, CDS having less than 300 nucleotide were excluded.
Now how should we proceed to estimate total number of nucleotides in the final data set without doing it manually?
Hi Nimal
When you retrieve your DNA sequence from NCBI there is an option to highlight only the CDS and it also shows the coordinates (beginning and ending) of the coding sequences. retrieve the fasta file of the CDS by inserting the coordinates into an option located at the top right corner of the NCBI " Change region shown" . then the number of nucleotides can be obtained by subtracting the starting coordinate from the ending coordinate.
If you saved your cds in a fasta file on your computer, and you are on a unix/linux computer with the Emboss package installed (http://emboss.sourceforge.net/), then running infoseq will compute the length of each sequence and return that in tabular format.
a simple way to open in BLAST2GO -- see according to size -- export after unclicking undesired and export into fasta.
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