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interpreting search results...HELP!

bickle at urz.unibas.ch bickle at urz.unibas.ch
Wed Mar 16 09:00:21 EST 1994

In article <robison1.763745001 at husc10.harvard.edu>, robison1 at husc10.harvard.edu (Keith Robison) writes:
> brett at BORCIM.WUSTL.EDU writes:
> On another note, a constant annoyance for me is the fact that many
> authors do not sufficiently document the methodology used.  For example,
> target databases are not specified explicitly ("no matches were found
> by database searches") or versions are not stated ("no matches were found
> in GenBank").  For BLAST & FASTA searches, the substitution matrix
> used is not specified (this was a glaring flaw in a comparison of
> search methods posted recently). People don't publish Southern's or
> in situs without specifying the conditions; why are computational methods
> any different?
>>it will help a lot of people to utilize these methods to their fullest,
>>without overinterpretting the results. Thanks in advance...
> Keith Robison
> Harvard University
> Department of Cellular and Developmental Biology
> Department of Genetics / HHMI
> krobison at nucleus.harvard.edu 
Authors are not always to blame for the lack of detail in papers; editors
and reviewers have a lot to answer for. Two recent examples from my
own experience: gap weight penalties etc. disappeared from the figure
legend of a dotplot at the hands of a copy editor; a test of the 
significance of some comparative restriction results by Student's T test
stimulated a reviewer to demand that the methodology be detailed in
Materials and Methods and the editor to recommend its removal as
"the results are clearly significant".
Tom Bickle
Microbiology Dept, Biozentrum, Basel University
Klingelbergstrasse 70, CH-4056 Basel, Switzerland
+ 41 61 267 21 20       bickle at urz.unibas.ch

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