nucleotide sequence searching via the Internet

LERICKSO at CROP.UOGUELPH.CA LERICKSO at CROP.UOGUELPH.CA
Thu Mar 3 10:33:24 EST 1994


From:          kshinka1 at swarthmore.edu (Kanade Shinkai)
> Subject:       nucleotide sequence searching via the Internet
> Date:          1 Mar 1994 21:46:29 GMT

>
>
> Hello All,
>
> We have a short invertebrate nucleotide sequence that we wish to run
> against the various nucleotide data bases available on the Internet.
> We are aware that methods exists for doing this via e-mail (e.g.,
> NCBI-BLAST, FASTA, QUICKSEARCH, etc.) but have no experience doing
> this.  We have downloaded the help files which explain how to format
> search queries.  However, we are not familiar with the theoretical
> bases for these algorithms, and, therefore, do not understand the
> meaning of the various parameters used, and how they relate to more
> straight-forward sequence properties such as homology.
>
> Can anyone recommend how we should procede from here?
>
> Please send replies directly via e-mail, as we don't frequently peruse
> this group.  Thanks ahead of time for the help.
>
> Cheers,
> Kanade Shinkai

Good question. I recently looked at the two references given along
with the results of a BLAST search (Gish and States. 1993.
Identification of protein-coding regions by database similarity
search. Nature Genetics 3:266-72; Altschul et al. 1990. Basic local
alignment search tool. J. Mol Biol. 215:403-10) and did not find them
very helpful, i.e. they were not very lucid.
    Does anyone know of other references which explain BLAST better
and would be useful in the interpretation of the results of such a
search?
    By the way, why so I see so few references to BLAST is the
literature??








Larry R. Erickson,
Department of Crop Science,
University of Guelph,
Guelph, Ontario,
Canada  N1G 2W1
Internet: LERICKSO at CROP.UOGUELPH.CA
Fax: 519-763-8933  Phone: 519-824-4120 Ext. 3398



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