Difference between revisions of "Help:Search"

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== How to search for a basic part ==
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__NOTOC__
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{{HelpPage/GridCSS}}
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{{HelpPage/FindParts}}
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{{HelpPage/MainLinks}}
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<html>
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<style type="text/css">
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</style>
  
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'''(1)'''  If you know the '''''part number''''' (''e.g.'', BBa_J45001), simply type the unique characters after the underscore (J45001 in this case) into the '''"jump to part"''' search box under the Catalog icon on any Registry page. This immediately takes you to the Main Page for the part.
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<div class="container_12">
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<div class="grid_12">
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<h3>Search Tools</h3>
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</div>
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<div class="grid_7">
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<ul>
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<li>Know the part name (ex: </html><partinfo>BBa_E0040</partinfo><html>)? Type it into the <b>search field</b> <img src="https://static.igem.org/mediawiki/parts/4/4f/Registry_Menu_Search_Field.png" height="18px" /> on the Registry menu above, and go directly to the <a href="https://parts.igem.org/Help:Nav/Part_Main_Page">part's main page</a>.</li>
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<li>Hover over the gray triangle <img src="https://static.igem.org/mediawiki/parts/a/a6/Registry_Menu_Search_Drop.png" height="12px" /> next to the search field for the full search drop down menu, which has multiple <b>search options</b>.</li>
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</ul>
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<img src="https://static.igem.org/mediawiki/parts/0/02/Search_Drop_Down.png" width="450px" />
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</div>
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<div class="grid_5">
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<ul><b>The Registry has several search tools which let you find parts in different ways.</b>
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<li><a href="#Google_Site_Search">Google Site Search</a></li>
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<li>Go to this page (or create it)</li>
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<li><a href="#Get_help_in_assembling_this_part">Get help in assembling this part</a></li>
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<li><a href="#Find_parts_that_use_this_part">Find parts that use this part</a></li>
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<li><a href="#Find_parts_in_the_same_range_as_this_part">Find parts in the same range as this part</a></li>
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<li><a href="#Find_parts_that_contain_this_text">Find parts that contain this text</a></li>
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</ul>
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</div>
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<div class="clear"></div><br /><br />
  
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'''(2)'''  If you know the '''''name of the part''''' (''e.g.'', autoinducer synthetase), type this into the '''"Text Search"''' box below.  For autoinducer synthetase, at least seven hits will be displayed, from which you can select those of interest and click on their part numbers to go to the corresponding Main Pages.
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<div class="grid_12">
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</html>
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===Google Site Search===
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You can use a google site search for the <b>Registry</b> (parts.igem.org) and <b>iGEM</b> (igem.org)
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<html>
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</div>
  
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'''(3)''' If you know the '''''broad category''''' of the part you need, but not its exact name or part number, use the icons on the [https://parts.igem.org/wiki/index.php/Part_Types '''"Browse Part Types"'''] page.  Note that there are six categories of "parts" on this page: Systems, Devices, Parts, Chassis, Vectors and Other.  ''Basic parts'' are under the heading '''Parts'''.  [Note that the term "part" has two usages, reflecting the hierarchical classification scheme used by the Registry. In the broad definition, a "part" is a modular component of a synthetic-biology construct. A '''basic part''' comprises an indivisible functional unit (such as a protein-coding sequence or a terminator sequence).  A '''composite part''' has multiple basic parts within it -- for example, [https://parts.igem.org/wiki/index.php/Part:BBa_I13521 BBa_I13521] has five components, each of which is a basic part.]
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<div class="grid_7">
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</html>
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===Get help in assembling this part===
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'''Used for composite parts:''' (previously called subpart search)
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*The search will first breakdown the composite part into basic parts.  
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*Basic/composite parts matching portions of the composite part will be returned, along with a key showing the status/availability of the parts.  
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*This search will also show twins for your part.
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*You can enter multiple parts, but they need to be in the correct order.
  
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Click on the '''icon''' corresponding to the type of basic part that you need. This will take you to an intermediate page in some cases (such as "Protein Coding") with links to sub-categories. Otherwise the link goes directly to a page with '''tables of the parts''' in that category.  Depending on the type of part, the tables provide various kinds of information, always including a brief description and the total length of the part (in base pairs). Clicking on the part number in the table takes you directly to the Main Page for that part. Parts listed in these primary tables all have DNA available in the Registry, and those that have a "W" beside their entry have been shown to work in at least one system.
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'''Useful...'''
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*if you're putting together a new composite part.
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**You've added the part to the Registry and are going to assemble it in the lab.
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**Instead of assembling the entire part from basic parts, you can see if the Registry has intermediates. This will save you time in the lab.
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**You could assemble <partinfo>BBa_J04450</partinfo> from its five basic parts, or you could assemble <partinfo>BBa_R0010</partinfo> (basic part) with <partinfo>BBa_I13507</partinfo> (composite part).  
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<html>
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</div>
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<div class="grid_5">
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<img src="https://static.igem.org/mediawiki/parts/8/80/Help-Loc-Subpart-Search.png" width="380px" />
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</div>
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<div class="clear"></div><br />
  
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Note that at the tops of the main tables for parts there are a clickable links entitled ''"Show __ more parts"'' (where the blanks correspond to numbers from 0 to hundreds).  The links will take you to subsidiary tables of '''parts in various stages of design and development''', usually with the planned DNA sequence, but without availability of the physical DNA or evidence for workability.
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<div class="grid_7">
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</html>
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===Find parts that use this part===
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'''Find all the composite parts (and twins) that use your part''' (previously called superpart search)
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*Parts with available samples will appear at the top of the search results.
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*You can enter multiple parts, but they need to be in the correct order.
  
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'''Useful...'''
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*if you've found that a sample of your part is not available or has poor quality control.
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**you can find an available confirmed composite part containing your part, and [[Help:Protocols/PCR_Standardization|PCR it out]]
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*if you want to find composite parts that contain your basic (or composite) part
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<html>
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</div>
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<div class="grid_5">
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<img src="https://static.igem.org/mediawiki/parts/d/dc/Help-Loc-Superpart-Search.png" width="380px" />
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</div>
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<div class="clear"></div><br />
  
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== How to search for a composite part ==
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<div class="grid_7">
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</html>
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===Find parts in the same range as this part===
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Search for parts with names following this part. Enter a part name such as BBa_K123456 and the software will find up to 1000 parts with a name like BBa_K123xxx where the part name is equal to or beyond BBa_K123456. (previously called 1000 part range search)
  
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The same methods described above in '''(1)-(3)''' can also be used to search for devices and systems. These always have multiple basic parts and that allows another approach --
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*This search can be used for identifying all parts that an iGEM team or lab have added. Each iGEM team or lab group is given a range of part names ('''Ex.''' BBa_K123000 - BBa_K123999) to use when they've registered.
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**Use if you've found an interesting part, ('''Ex.''' BBa_K123008)  and want to see other parts that the team or lab created within that specific part range
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**By entering BBa_K123000, the search will return results for all parts between BBa_K123000 - BBa_K123999.
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*This search also shows what parts have available samples
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<html>
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</div>
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<div class="grid_5">
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<img src="https://static.igem.org/mediawiki/parts/a/ac/Help-Loc-1000-Search.png" width="380px" />
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</div>
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<div class="clear"></div><br />
  
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'''(4)'''  If you want a '''composite part that contains a particular basic part''', such as [https://parts.igem.org/wiki/index.php/Part:BBa_C0051 cI repressor from phage lambda], you can enter the part number into the '''Superpart Search''' box below.  In the case of that example, the search returns more than 300 parts, of which more than 60 are available in the Registry!
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<div class="grid_7">
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</html>
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===Find parts that contain this text===
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Search for a word or phrase. This text search will look through the short description (S:), description (D:), notes (N:), and author (A:) of parts to return your results.
  
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== How to find alternative ways to construct a composite part ==
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'''The text search is particularly useful if you...'''
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*do not know of a specific [[Help:BioBrick_Part_Names|part name]]
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*know a descriptor of the part (e.g., red fluorescent protein)
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*know who may have made it
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*know what it may have been used for
  
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'''(5)''' If you have a '''composite part''' that poses some difficulty in assembly or function you can examine '''alternatives''' by using the Subpart Search box below. Note the link above the box -- it displays a good example of the power of such a search.
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'''A few things to remember...'''
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*You may want to try a few variants of the description of the part, e.g., RFP; red fluorescent protein, etc.
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*This search is nonspecific: you may be returned results including basic parts, intermediate parts, devices, etc. You may find that some results only have references to your part, instead of including the part itself.
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**'''Example:''' ''<partinfo>BBa_I722012</partinfo> - D: this part could accept AHLs and also '''could''' produce mRFP easily to detect'' as opposed to ''<partinfo>BBa_I722015</partinfo> - D: produce both mRFP and rhiR protein''
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*Not setup to show part availability
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*You can also do a text search using a part name (BBa_E1010 or E1010 for mRFP)
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<html>
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</div>
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<div class="grid_5">
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<img src="https://static.igem.org/mediawiki/parts/d/d9/Help-Part-Search-Text.png" width="380px" />
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</div>
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<div class="clear"></div>
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</div>
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<div class="clear"></div>
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</html>
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{{HelpPage/FAQ/Search}}

Latest revision as of 21:52, 15 June 2017

Search Overview

Use a variety of search tools to find interesting and useful parts.

Catalog Overview

Browse through the Registry by part type, curated collections, most used parts, and more!

Browse Distribution

See all the part samples that are in your Distribution Kit, along with their quality control results.

Search Tools

  • Know the part name (ex: BBa_E0040)? Type it into the search field on the Registry menu above, and go directly to the part's main page.
  • Hover over the gray triangle next to the search field for the full search drop down menu, which has multiple search options.


Google Site Search

You can use a google site search for the Registry (parts.igem.org) and iGEM (igem.org)

Get help in assembling this part

Used for composite parts: (previously called subpart search)

  • The search will first breakdown the composite part into basic parts.
  • Basic/composite parts matching portions of the composite part will be returned, along with a key showing the status/availability of the parts.
  • This search will also show twins for your part.
  • You can enter multiple parts, but they need to be in the correct order.

Useful...

  • if you're putting together a new composite part.
    • You've added the part to the Registry and are going to assemble it in the lab.
    • Instead of assembling the entire part from basic parts, you can see if the Registry has intermediates. This will save you time in the lab.
    • You could assemble BBa_J04450 from its five basic parts, or you could assemble BBa_R0010 (basic part) with BBa_I13507 (composite part).


Find parts that use this part

Find all the composite parts (and twins) that use your part (previously called superpart search)

  • Parts with available samples will appear at the top of the search results.
  • You can enter multiple parts, but they need to be in the correct order.

Useful...

  • if you've found that a sample of your part is not available or has poor quality control.
    • you can find an available confirmed composite part containing your part, and PCR it out
  • if you want to find composite parts that contain your basic (or composite) part


Find parts in the same range as this part

Search for parts with names following this part. Enter a part name such as BBa_K123456 and the software will find up to 1000 parts with a name like BBa_K123xxx where the part name is equal to or beyond BBa_K123456. (previously called 1000 part range search)

  • This search can be used for identifying all parts that an iGEM team or lab have added. Each iGEM team or lab group is given a range of part names (Ex. BBa_K123000 - BBa_K123999) to use when they've registered.
    • Use if you've found an interesting part, (Ex. BBa_K123008) and want to see other parts that the team or lab created within that specific part range
    • By entering BBa_K123000, the search will return results for all parts between BBa_K123000 - BBa_K123999.
  • This search also shows what parts have available samples


Find parts that contain this text

Search for a word or phrase. This text search will look through the short description (S:), description (D:), notes (N:), and author (A:) of parts to return your results.

The text search is particularly useful if you...

  • do not know of a specific part name
  • know a descriptor of the part (e.g., red fluorescent protein)
  • know who may have made it
  • know what it may have been used for

A few things to remember...

  • You may want to try a few variants of the description of the part, e.g., RFP; red fluorescent protein, etc.
  • This search is nonspecific: you may be returned results including basic parts, intermediate parts, devices, etc. You may find that some results only have references to your part, instead of including the part itself.
    • Example: BBa_I722012 - D: this part could accept AHLs and also could produce mRFP easily to detect as opposed to BBa_I722015 - D: produce both mRFP and rhiR protein
  • Not setup to show part availability
  • You can also do a text search using a part name (BBa_E1010 or E1010 for mRFP)

I'm looking for a part or device but I don't know the part name

You can browse the Catalog of Parts & Devices or do a Text Search. The Catalog organizes the available parts of the Registry by various criteria and a Text Search will let you search using a descriptor.

I know my part's name and want to go to its main page

If you know the part name (e.g., BBa_J04450), simply type the name (BBa_J04450, or J04450) into the search box at the top right corner of the Registry and hit enter (or click Go). This immediately takes you to the Main Page for the part.

I want to find composite parts that contain my basic (or composite) part

You'll want to do a Superpart Search which will list all the composite parts containing your part of interest. The parts that are available from the Registry will appear at the top of the search results. You can enter multiple parts, but they need to be in the correct order.

I'm putting together a composite part and would like to find any intermediaries

You may find yourself putting together a composite part made of several basic parts. Before you begin assembling your part in the lab you'll want to use the Subpart Search which will show you whether there are any parts in the Registry that match a portion of your composite part.

I've found a part that I'd like to use but it's unavailable

  • Twins
  • Related Parts
  • Part search tools