problem with blasting on ncbi - (Apr/10/2013 )

Dear all,

I would like to blast/compare a sequence (one that I have) with one that is avaible on ncbi.
How can I do this in the most elegant way?

The problem is that I do not seem to find a way to download the entire sequence to use it on http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=blast2seq
(blast2sequences)

When I download the fasta format of the organism from ncbi I get a file with all the contigs, however they are interupted with
">gi|381420886|gb|AFNH02002571.1| contig03417, whole genome shotgun sequence" statements".
(statement sequence statement sequence.. it goes on like that rather then having 1 big sequence taped together)
So when I try to copy and paste the genome into the website it only checks the first sequence with my sequence rather then checking the entire sequence.
Is there an alternative to check my sequence with the one form ncbi?
Or is there an easy way to remove those statements from the file?

It is this sequence-

Gregarina niphandrodes contig03417, whole genome shotgun sequence

Right?..Did you copy the FASTA sequence and paste on blastn?..I tried it worked..I dint see any problem..here is the sequence-

http://www.ncbi.nlm.nih.gov/nuccore/381420886?report=fasta
just copy and paste....hope it will work

neuron on Wed Apr 10 12:21:43 2013 said:

No its not.
This is part of the whole genome.
The whole genome is cut up in little parts (like this one).
I would need the entire genome, not just a part.