Free software in molecular biology draft document

Rodrigo Lopez rls at ebi.ac.uk
Fri Jun 26 11:38:44 EST 1998

Dear Dr. Gilbert,

Just having glanced through the draft I noted the following things which I
think should be added or amended for completeness sake:

1. There are no examples commercial packages. But maybe this is intentional
from your side. It would be useful to mention a few just for the sake of
comparison and to make the reader aware that, quite often, free programs are
a reflection of lacks in commercial packages :-)

2. On the section on Internet Resources you mention the EBI and P. Rodrigues
Biocatalog. Could you include the URL to it?


3. Since you mention NCBI's Entrez, I think it is fair to mention SRS as
well :-)

4. The mention of Peter Rice's EMBOSS: Just talked to Peter Rice and he
tells me he will not do a VMS but possible other will be interested enough
to do it as well as Windows NT! :-)

5. You mention RasMol2 specifically. It is a great piece of software but
today one should consider, and many are Swiis-PDB Viewer which does quite a
bit more than Rasmol does:


6. While a lot of development is going on in the multiple sequence alignment
front and general sequence analysis, there is.. the matter of database
searching, which will ultimately become a centralised service for many
database providers. This because of the size of the databanks and the
expense of large multiprocessor servers required to run these efficiently.
Links to:

NCBI - blast
EBI  - blast2   : http://www2.ebi.ac.uk/blast2/
EMBL - blast2   : http://www.bork.embl-heidelberg.de/Blast2/
ISREC- blast2   : http://ulrec3.unil.ch/software/WUBLAST_form.html
EBI  - Fasta3   : http://www2.ebi.ac.uk/fasta3/
EBI  - scanps   : http://www2.ebi.ac.uk/scanps/
EBI  - ssearch3 : http://www2.ebi.ac.uk/ssearch3/
EBI  - clustalw : http://www2.ebi.ac.uk/clustalw/

As I said earlier I just glanced through the draft very quickly and thought
I'd mention the above. I will go through it carefully and hopefully get back
to you next week.

Yours sincerely,


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