[EMBOSS] Seqret fetch by URL

[Steve Taylor]

Hi,

I am trying to fetch a sequence using seqret. In my EMBOSS defaults I have the following entry set up. I am using EMBOSS 6.0.1 both on Linux and Solaris.

DB NCBI_prot  [  method: url  format: fasta  type: P
   url: "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr
om=begin&to=end"
   comment: "NCBI protein - FASTA seqs only"
]

If I try:

seqret NCBI_prot:ACA69081

I get:
Reads and writes (returns) sequences
Error: Unable to read sequence 'NCBI_prot:ACA69081'
Died: seqret terminated: Bad value for '-sequence' and no prompt

However, if I try

http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=ACA69081&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end

I get

>gi|169751563|gb|ACA69081.1| glycoside hydrolase family 1 [Yersinia pseudotuberculosis YPIII]
MSYQQLPKDFLWGGAVAAHQVEGGWDKGGKGVSIADVLSGGSHGVDRVMTDGVLEGYRYPNHEAVDFYSH
YKEDIALFAEMGFKCFRTSIAWTRIFPHGDEQQPNEAGLQFYDDMFDELLKYGIEPVITLSHFEMPWHLV
KEYGGWKNRKVVDFFVKFSEVVMARYKSKVKYWMTFNEINNQRNWKYPLFGYCCSGVVFTEQENPEETLY
QVLHHQFVASAKVVKLGHAINPEFKIGCMVAMVPLYPFSCHPDDMMYSVEAMRERYLFGDVHMRGYYPSY
ILQEWARRGFNIHMEEGDLETLRDGCADYMGLSYYMSNAVSAINPGSGNSLSGFEGSVPNPHVKASDWGW
QIDPVGLRYSLSVLYERYQKPLFIVENGFGAIDKVAADGMVHDDYRIAYLKAHIEQMKKAVFEDGVDLMG
YTPWGCIDCVSFTTGEYSKRYGFIYVDKNDDGTGTMARSRKLSFDWYKKVIASNGEVL


Any ideas why or is there a way I can get more verbose information about what is going on?

Thanks,

Steve