Notes from ACEDB Workshop, part I

Sonnhammer E./Durbin esr at al.mrc-lmb.cam.ac.uk
Wed Sep 22 11:40:05 EST 1993

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

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