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Help with sequence searching

Mike Cherry cherry at stout.Stanford.EDU
Sat Oct 1 00:05:06 EST 1994


In article <Cwz4uI.LuB at news.cis.umn.edu>,
Dubear Kroening <dubear at molbio.cbs.umn.edu> wrote:
>
>I was hoping someone could help me with sequence searching of the yeast
>chromosomes.  Being (somewhat) ignorant with computers, how would I go
>about searching S. cerevisiae Chromosomes II and XI using a DNA seq. that
>I have obtained.  I can't get either of these in our version of fasta,
>perhaps it is not yet updated.  I tried downloading the yeast Chr XI seq.
>(in GCG format) and comparing it to my seq., but it wasn't readable.

    The chromosome III sequence is the only chromosome sequence that
is available in one piece from the sequence databases.  The entire
sequence of chromosomes II, VIII, and XI are present in the databases
but as subchromosomal size pieces.  If you search the current GenBank
or EMBL databases you will be searching all of II, III, VIII, and XI.
For chromosome II and XI the sequence is present in overlapping gene
size pieces.  For chromosome VIII the sequence is present in cosmid
clone size pieces.  Tables of the sequence entries are available
through anonymous ftp from a variety of servers as previously
announced in this group (ftp.ebi.ac.uk; ftp.embl-heidelberg.de;
ftp.pasteur.fr; ftp.mips.embnet.org; ncbi.nlm.nih.gov) including
genome-ftp.stanford.edu and through Gopher from
genome-gopher.stanford.edu.

    The problem you encountered with the GCG file is most likely its
size.  GCG version 7 has a default maximum limit of 350,000
nucleotides per sequence.  Thus the complete sequence of chromosomes
II, VIII, and XI are too large.  This limit can be increased by your
system manager. The procedure is described in the GCG managers
documentation.

    Files with less than 350,000 nucleotides in GCG format are
available for the four currently finished chromosomes from the
Stanford servers mentioned above.  I just added the chromosome VIII
and XI files today.  The chromosome II split files were part of the
files produced with its release by Horst Feldmann et al. (1994) EMBL
J. and H. Werner Mewes, MIPS.

    From the Gopher server genome-gopher.stanford.edu select:

     -->  5.  Saccharomyces Information/

    Then

      -->  6.  S. cerevisiae Genome Sequencing Results/


Mike
--
J. Michael Cherry
cherry at genome.stanford.edu
Department of Genetics
Stanford University

     Contacts for the Saccharomyces Genome Database Project (SGD)
             e-mail:    yeast-curator at genome.stanford.edu
                ftp:    genome-ftp.stanford.edu
             Gopher:    genome-gopher.stanford.edu
                WWW:    http://genome-www.stanford.edu/



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