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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
