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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