What's New In SGD in 1998?
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December 11, 1998
December 4, 1998
- SGD has added a link to the Yeast Cell Cycle Analysis Project detailing the study by
Spellman, et al. (Comprehensive Identification of Cell
Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by
Microarray Hybridization (1998) Molecular Biology of the Cell 9,
3273-3297).
December 3, 1998
November 20, 1998
- A table of 27 new ORFs added by SGD based on its analysis of
the SAGE data of Velculescu,
et al., (1997) Cell 88:243-251. It includes links to relevant
information about each ORF and the data used to identify it.
November 9, 1998
- A list of yeast
introns provided by the Ares Lab at the University of California, Santa Cruz is now available.
September 14, 1998
August 14, 1998
- Deletion strains created by the Saccharomyces Genome
Deletion project are available via Research Genetics. There are
currently 676 ORF deletions available, with deletions on chromosomes
I, V, VIII, XIII and XV.
July 27, 1998
July 6, 1998
- The program and abstracts for the Yeast
Genetics and Molecular Biology Meeting are now available. The
abstracts can be searched by keywords or by concepts. The meeting will
be held at the University of Maryland, College Park, from Tuesday,
July 28, through Sunday, August 2.
June 25, 1998
- Using
Gene/Sequence Resources: SGD curators have written a tutorial to
show users how to use Gene/Sequence Resources to retrieve DNA and
protein sequences, homologies, restriction maps, biological
information and more.
June 19, 1998
- Global Gene
Hunter has been modified to allow you to search SGD, GenBank and
PubMed for gene name aliases that are known to SGD.
- Finding
an ATCC Clone That Overlaps a Gene: SGD has updated this Hot Tip
to show how the use of new SGD software (Gene/Sequence
Resources) makes it simple to identify an ATCC clone that contains
a sequence of interest.
May 7, 1998
- Gene/Sequence
Resources is a new tool that serves as a central jumping-off point
for obtaining information on your gene or sequence of interest. It
replaces our previous "Seq and Display". You provide Gene/Sequence
Resources the name of your gene or sequence, chromosomal coordinates,
or raw DNA or protein sequence, and then click submit. Gene/Sequence
Resources will then present a list for all the available options at
SGD for analyzing or displaying information about that gene or
sequence. Even better, Gene/Sequence Resources will save you time by
automatically pasting in sequences when performing BLAST or other
analyses, and it will take you to the standard name for a gene when
you type in an alias. Bookmark this page and save time.
-
The Genome-wide
Protein Similarity View allows you to display all the ORFs in the
S.cerevisiae genome that display similarity to one or more input
ORFs. You can enter ORF names or gene names and access graphic or
table displays of S. cerevisiae ORFs that demonstrate similarity based
on a genome-wide Smith-Waterman sequence analysis.
March 12, 1998
-
PubMed
searches via SGD now permit the option of "exploded" searches that
take advantage of NCBI MeSH terms. This may result in a larger number
of PubMed search results than if you were to perform an "unexploded"
search.
March 10, 1998
-
You can now search DNA sequences upstream of coding regions using
SGD's UTR (untranslated regions) datasets. The three datasets include
the DNA sequences that are 500, 1000, or 2000 basepairs upstream of
all defined ORFs in the systematic S. cerevisiae genomic
sequence. The UTR datasets are available for BLAST,
FASTA
and PatMatch
searches.
March 9, 1998
-
SGD releases SacchDB version 4.11, using the ACEDB
software (version 4.5) developed by Richard Durbin and Jean
Thierry-Mieg. SacchDB version 4.11 is available for UNIX systems.
Although SGD recommends using the WWW version of our database (it is
more frequently updated and contains information that is unavailable
in SacchDB), you can download a copy of the SacchDB database using
Anonymous FTP [Note (11/21/02): SacchDB is no longer available via ftp
(see obsolete
SacchDB FTP site; for downloading data from the current database,
please see Anonymous FTP
available on our Download Data
page.]
February 10, 1998
February 6, 1998
-
SGD has reorganized some of its WWW pages to emphasize information
about and from the yeast community. Please refer to our new page, Yeast
Community Information page. This page is no longer available. It has been replaced by the new Community Information page. (November, 2002)
- A new tool has been added to SGD's set of programs for sequence analysis! The Yeast Genome Restriction Analysis allows you to perform a restriction analysis on a input sequence or the sequence of an ORF, gene, clone or GenBank sequence you identify by name.
February 2, 1998
-
The SGD BLAST
search has been modified to use the "dust" filter by default for
nucleic acid query searches. The dust filter masks out simple repeat
and high AT rich regions from the query sequence. The resulting
sequences contains Ns at the masked positions. This masking or
filtering allow the search to go faster and possibly report more
relevant hits. With all the simple repeats removed you can more easily
see hits of the unique regions of your sequence. If you wish to turn
the filtering off, just select "none" from the Filter Options menu on
the BLAST form.
- SGD has assumed the responsibility for maintaining the list of
Saccharomyces cerevisiae lab URLs. The list, Links
to Saccharomyces cerevisiae Labs was maintained by Ramon Tabtiang
in the Herskowitz lab until February 1998. Many thanks to Ramon for
such a great resource!
January 1, 1998
-
The NAR database issue features a paper contributed by the SGD staff that details some of out latest improvements and innovations. See:
- Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database.