maize ESTs NCBI

Question

[dinesh]

My question looks simple but I'm new to bioinformatics. I have a task of downloading maize ests which are around 20 lakhs. So, how can I download this ESTs in batches?

For example: 50000 ESTs in one file and next 40000 ESTs in one file like wise.

Thanks in advance

Answer 1

[Pierre Lindenbaum]

Go to http://www.ncbi.nlm.nih.gov/nucest?term=%22zea%20mays%22[Organism]

Select 'send to -> file -> fasta ' & download

Use awk to produce sequences with two lines (name+header) and split

awk '/^>/ {if(NR>1) printf("\n"); print;next;} {printf("%s",$0);}' your.fasta  |  split -l 100000 - prefix