databases search - protein size

bionet at cgmvax.cgm.cnrs-gif.fr bionet at cgmvax.cgm.cnrs-gif.fr
Tue May 10 03:08:19 EST 1994


>: >
>: >I'm trying to find a way of searching databases for proteins (ideally from
>: >E.Coli) with a mass in a given range (say between 10 and 18 kDa).
>: >
>: ATLAS will do exactly this.
>.....
>
>: Use the command SELECT which, at the moment, is not documented...

>
>I am not sure about the documentation but it is required to write out
>the file of sequence names, and use additional software, as ATLAS does
>(as far as I know) no homology searches. ATLAS does NOT work with
>SWISSPROT, as this database is not on the CD (as there are no real DNA
>databases on the CD, either).
>

1) right, ATLAS does no homology searches. But the question was to retrieve 
sequences according to their MW, not to compare them to databanks. And the 
SELECT option of ATLAS answers the question. To my knowledge, ATLAS is 
the only software to do this - as well as, for example, retrieving all the 
sequences having an (Asp + Glu) content between 13 and 21%. Very useful.

2) right, ATLAS does not work with SWISSPROT. So what? The PIR CD-ROM 
contains the PIR protein databank. For sure, it is more redundant that 
Swissprot - more exhaustive? The last PIR release (PIR1 + PIR2 + PIR3 + 
PATCHX) contains more than 100,000 protein sequences. Again, ATLAS answers 
the question that was addressed.

3) The PIR CD-ROM contains an ECOLI databank which can be searched with 
ATLAS and, therefore, seems perfectly adapted to the original question ...

Jean-Loup


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