Human Genome Database

francis at NCBI.NLM.NIH.GOV francis at NCBI.NLM.NIH.GOV
Tue Dec 3 18:02:08 EST 1996

> From mthom0 at service1.uky.edu Tue Dec  3 17:22:13 1996

> Gerard Pujadas wrote:
> > 
> >         Dear netters, I'm sorry if I've posted the mail in an unapropiate
> > list. I would like to know if the human genome sequences are available as
> > part of the GenBank or there is an specialized DataBank for them. In that
> > case, where may I ftp the document which contains the human genome. 
> 	You can access human genomic sequences via NCBI at:
> http://www.ncbi.nlm.nih.gov/BLAST/
> 	Just enter your search sequence and choose "gss" as the database to
> search.  Alternatively, if you want to search for a specific gene or
> chromosomal location, hit the NCBI logo at the top to go to their home
> page, and there will be other search options for genbank.

Users should note that the 'gss' database is a subset of GenBank which
probably does not includes the types of sequences you are looking for.
(text from gbrel.txt when GSS was introduced attached below).  Note
that the gss division is not really (yet) that much comprehensive (only
a few thousand records).  If you want to find something, maybe better
to use the nr database.

And a protein search (protein/protein:blastp or
nucleotide_translation/protein:blastx) is always more sensitive than a
nucleotide/nucleotide:blastn search (specially if you are looking for
similarities across species)



| B.F. Francis Ouellette  
| GenBank Coordinator
| francis at ncbi.nlm.nih.gov   

> 1.3.3 New GenBank Division in Release 96.0
> A new division, GSS (Genome Survey Sequence), has been added 
> to the GenBank Flatfile release distribution; the file name is 
> gbgss.seq .
> This new division is similar in nature to the EST division, except that
> its sequences are genomic in origin, rather than cDNA (mRNA). The GSS
> division contains (but will not be limited to) the following types of
> data:
>  - random "single pass read" genome survey sequences.
>  - single pass reads from cosmid/BAC/YAC ends
>     (these could be chromosome specific, but need not be)
>  - exon trapped genomic sequences
>  - Alu PCR sequences
> Many labs have approached GenBank over the last few months, interested
> in submitting these types of sequences.  We have been reluctant to
> introduce them via the existing GenBank divisions.  On the other hand,
> such sequences are of value to the genome community, and require
> similar processing and access tools as have been provided for EST's and
> STS's. GSS sequences will will be used, amongst other things, as a
> framework for the mapping and sequencing of genome size pieces which
> will be present in the standard GenBank divisions.
> Sequence data appropriate for the new GSS division are, to date,
> generated by genome labs performing human genome sequencing; we expect
> that similar data will be generated for other model organisms, such as
> the mouse.

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