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| CRT home > Arcadia: Query for wildtype and mutant proteins |
Query for wildtype and mutant proteins:
This is the main entry page into Arcadia. It allows the user to query the database for both mutants
and wildtype proteins which are stored there. There are a number of different pulldown menus,
which can allow the user to refine their query to be able to find the entry of interest more
quickly and efficiently.
Clicking the Search button will retrieve a list of matching entries, which can then be viewed in more detail.
There are three main ways of refining your query: keyword in a field, by organism, and whether you want a mutant or a wildtype protein.
 | [ The wildtype/mutant protein pulldown menu ] |
You can choose to retrieve only wildtype proteins matching your query, only mutant proteins, or both.
| [ The organism pulldown menu ] |
You can refine your search so that only wildtype and/or mutant proteins
(depending on your selection from the pulldown menu desribed above) from this organism are returned
if they match your query.
| [ The field pulldown menu ] |
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Keyword in protein name [name]
The names of all the wildtype proteins in the database are searched to see if they
match the keyword given. If the keyword box is left blank, all wildtype and/or mutant proteins
are returned.
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Keyword in family name [family]
The family names of all the wildtype proteins in the database are searched to see if they
match the keyword given.
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Keyword in description [desc]
The user-given descriptions of all mutant proteins are searched for a match to the keyword
given. If the user has chosen to retrieve wildtype proteins, the wildtype proteins from which the
mutant proteins that match the description keyword are derived are returned.
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Accession code [ac]
The accession codes from external databases (such as Swissprot or Genbank) which are
associated with the wildtype proteins in Arcadia are searched.
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Mutant ID [mid]
The Arcadia mutant IDs are searched. IDs can be entered either as 'dlm1000' or as the
number alone '1000'. When using this option, the organism option is ignored. Again, if the user
has chosen to retrieve wildtype proteins only, the wildtype protein associated with the mutant
which has this ID is returned.
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Submitter [submitter]
The submitter field is searched. The name of the submitter must be entered exactly
as it appears.
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Position [position]
There are three ways of searching using the position option: by absolute position
(e.g., 167), generic position, (e.g., 3.50), or by whole transmembrane domain (e.g., TM6).
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Advanced
This option allows you to use a combination of the options above in one query text
field, e.g., dopamine[name] transporter[name] 3.50[position] (with no spaces between the keyword
and the option). The relevant terms to put in square brackets are given after each field in
the above list.
| [ Sorting the results ] |
The sort pulldown menu allows the user to sort the resulting entries. This is especially
useful when there are many entries returned. The default method of listing entries is
by their Arcadia ID. Entries can also be sorted by protein name (alphabetically), family
name (alphabetically), organism (alphabetically, by Latin name), submitter (alphabetically),
mutation (absolute position) and journal (first author name, journal name, and year).
Sorting by mutation and journal is only effective for mutant proteins.
go to next help page.
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March, 2012; Michelle Sahai, Ph.D., a Postdoctoral Associate in Harel Weinstein's lab, was awarded a three year Canadian Institutes of Health Research (CIHR) Fellowship for her research on Molecular Mechanisms of the Dopamine Transporter Function: The effects of drugs of abuse.
Feb, 2012; Sayan Mondal, a student in Harel Weinstein's lab, won the Student Research Achievement Award at the Biophysical Society's 2012 Annual Meeting for his poster on the interaction of GPCRs with the membrane.
Jan, 2012; Jan Dlabal, a student from the Lycée Français de New York, was selected as a semi-finalist in the 2012 Intel Science Talent Search, for work on the determination of large-scale genomic structure performed in the lab of Olivier Elemento.
Oct, 2011; Sheila Nirenberg presented a talk, "Can we speak the language of the brain?", at the TEDMED 2011 conference.
A Q & A session followed.
Nov, 2011; GobyWeb binary release. The Campagne laboratory has just released a binary distribution of GobyWeb. This first public release of GobyWeb makes it possible to install the tool locally for non-commercial use. Detailled installation instructions are available on the download page.
Apr, 2011; Dr. Olivier Elemento was awarded an NSF CAREER Grant, the National Science Foundation's most prestigious award in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research.
Nov, 2010; Dr. Sheila Nirenberg's work on artificial retinas has been featured in Technology Review, Wired, Scientific American, and the New Scientist.
Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
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