How To Build The Correct Blast Url For The Rest Interface

Hi All,

I am having difficulties constructing a BLAST query via the REST interface.

In particular I would like to have a defline via QUERY_BELIEVE_DEFLINE and actually submit two sequences.

The URL I construct is this (BTW, apparently the URL is to long for the forum): http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY_BELIEVE_DEFLINE=yes&QUERY=%3E%20PMID%2019846642%20Forward%0D%0AATGTTCGATTCCGGCTTCC%0D%0%3E%20PMID%2019846642%20Reverse%0D%0CGGGCTTCGGTGTACCTCAT&PROGRAM=blastn&DATABASE=nr&ENTREZ_QUERY=gyra%20[gene]%20AND%20AL123456.3%20AND%20txid83332%20[ORGN]&CMD=PUT

When I look at the query in the BLAST website interface, the Query Sequence looks like this:

>19846642 Forward
ATGTTCGATTCCGGCTTCCMDRVRSGGGCTTCGGTGTACCTCAT

What I really want is my Query to look like this:

>PMID 19846642 Forward
ATGTTCGATTCCGGCTTCC>PMID 19846642 Reverse
GGGCTTCGGTGTACCTCAT

So it looks like the hex conversion somehow kinda worked but also kinda did not work.

What am I doing wrong in my query construction ?