Thanks John McCarthy for your excellent notes of the ACEDB workshop!
I feel obliged, however, to correct your notes on 'fetch' which
retrieves sequence data from external databases for either annotation
pop-up or multiple alignment of blast segments in 'Blixem'.
Your notes say:
> Sequence Fetch/Align
> --------------------------
> a. summon up SwissProt/PIR entry(s)
> b. show multiple alignment based on BLAST segments = BLIXEM
> uses unix command
> fetch -Bdbname (SP,PIR,EMBL,GB)
> -a accession number
> -P Pearson (FASTA) format
> -s just sequence ... no new line
> our version uses the EMBL CDROM index structure
The -P and -s options are incorrect. They should be
-f Pearson (FASTA) format
-q just sequence (on one line)
The fetch program used here in Cambridge is available by anonymous FTP
on cele.mrc-lmb.cam.ac.uk in /pub/acedb/fetch.tar.Z, which contains
further instructions. There are actually about 15 options at the
moment. If you prefer to call your own 'fetch' from ACEDB, only the
-q option is necessary though.
Erik Sonnhammer
Sanger Centre
Cambridge, UK
