Enter the name of your marker in the box provided. You can type the full name, or just the first few characters (for example, typing "GATA" will bring up a list of all markers in the CHLC database beginning with those letters). Hit enter, or click on the "search" button.

A list of all markers matching your search parameters will be displayed, followed by additional information about those markers. This will usually consist of:

• The name of the marker
  
• Also known as: most markers have multiple names. See Help with Nomenclature for more details.
• A long list of maps. These can be informative, but are often very long. They are usually genetic maps of the entire chromosome your marker is located on.
  
• Primer sequence, PCR conditions, etc. You will only get this information if it is in the CHLC database. Don't despair if it isn't - there are plenty of other places to look.
  

If the CHLC search finds no matches to your marker, either try a different search, or try again with a less specific name, or a different one. You can use the search index at the bottom of the "sorry" notice, rather than going back to Nifty each time.

Enter your marker name in the box. It must be entered exactly, with no extra spaces or wildcard characters (although upper and lower case don't matter). Hit the enter key or the "search" button.

The first screen you'll get should show the marker and the YACs positive for it. One of the names of the marker will be a hyperlink. Click on that, and you'll get a second screenfull of info.

The second screen should have more detailed information about your marker. This may include primer sequence, number of alleles, heterozygosity, and a few links to additional data.

The links will take you to:

• Marker: this takes you back where you were. Don't bother.
  
• LOCUS: this is a GDB search on your marker. For help with that, see GDB Help.
• EMBL: this searches the EMBL gopher. I haven't had much luck doing that, but feel free to try.
  

Type what you're looking for in the box. This can be the name of a marker or gene, the chromosome location it's on, or a phrase associated with it. This amount of flexibility makes this the most broad-based search form accessed by Nifty. Beware, though, broad searches can often return far more information than you want.

You don't need to worry about the radio buttons on the bottom of the form. The default is "both databases." If you are only interested in information that was recently published, select "updates only."

When the search returns your results, they will be separated into two sections, one for each database. Be sure to scroll to the bottom of the screen - just because the first database came up empty doesn't mean there's no data waiting for you below.

A list of your matches will appear, each with a small square graphic to click on, and a brief description of the result. If you get too many returns, try narrowing your search parameters. You may want to access the full Genbank search form which will allow you to select multiple search terms and field restrictions. For example, if a particular search brings up 2 interesting genes, and 25 genes from C. elegans, you can add a "human only" parameter - or a "not elegans" parameter.

Once you find the result you were looking for, selecting the link for it will bring up a screen chock-full of info. This will typically include the date the region was added to the database, the lab that sequenced it, the publication it originally appeared in, the sequencing method used, and the full sequence.

First, enter your marker name in the box provided. This can be an assay name, a locus name, or a GenBank accession number. Hit the search button or the enter key.

The screen that comes up ("Search for an STS by name") will show you the name you searched for in an entry box. There will be two radio buttons below it. Further down the screen will be a list of markers that matched your search. Hopefully, the one you were looking for will be on that list. Click on it to advance to the next page.

If no markers were found, try making your search more broad. Change the radio button selection from "exact" to "wildcard," and replace some characters with asterisks. For example, if a search for "GATA-P18625" came up negative, try "*18625" instead. Sometimes things like dashes vary from database to database.

The information on the next page should include:

• Database ID and other names (see Help with Nomenclature for more details on this.)
  
• Source - Historical information on the original publication data.
  
• Chromosome - Clicking on this will bring up a giant map of YAC contigs on that chromosome.
  
• Primers and product length
  
• Complete Sequence - click to see sequence data.
  
• Genbank ID - click on that to access Genbank data for that marker.
  
• Description - as listed in Genbank
  
• Search for GDB data - selecting that link will activate a GDB search for the marker. For help with that, see GDB Help
• Genetic Mapping Information
  • Physical mapping data in cM (usually from Genethon maps)
    
  • Radiation Hybrid Data - From the WICGR maps
    
  • YAC "hits" - lists of Yeast Artificial Chromosomes that give positive PCR results with this marker
    
  • YAC Contig Data - highly informative charts of data based on YAC PCR results, genetic mapping, physical mapping, and raditation hybrid data.
    NOTE: you must be using Netscape 1.1N or later to view these tables. On an older browser, they will appear as a jumbled mess of links.
    
  • For more information on how Contigs are assembled, see MIT's Guide to Contigs
    

Much of this information will be in hypertext form. Clicking on a YAC name, for example, will bring up huge amounts of information on that YAC. Clicking on the contig name will bring up data for that contig. Clicking on the name of a chromosome will bring up graphic maps of all contigs mapped to that chromosome. If you get lost in all the data, you can hit the "back" button on your browser to return to the original search data.

Enter the oligo sequence (and, optionally, its name) and hit the button. What could be simpler?

If you'd like more detailed information on what data to expect, and how that information is calculated, check out The oligo stat main page.

Enter the name of the YAC and press the search button (the enter key doesn't work here. Extra credit if you figure out why!)

If you're looking for more than one, enter them in the longer box, separated by spaces.

The search results will include:

• YAC name - which you already knew...
  
• Size as determined at MIT. This is rarely the same size you'll calculate yourself. It's a good gauge to separate small YACs from huge ones, but don't take it to be extremely factual.
  
• STS hits. These are polymorphisms, genes, and ESTs that should be positive for your YAC. These are determined by block pool screening, giving rise to three types:
  
  • Unambiguous - positive in block pool tests for this particular YAC
    
  • Disambiguated - positive for a range of YACs, including this one. Other YACs in this range have been excluded as false postives due to other mapping data.
    
  • Ambigious (use with extreme care) - positive for an inclusive range of YACs containing yours. Rarely informative.
    
• YAC Contig Data - highly informative charts of data based on YAC PCR results, genetic mapping, physical mapping, and raditation hybrid data.
  NOTE: you must be using Netscape 1.1N or later to view these tables. On an older browser, they will appear as a jumbled mess of links.
  
• For more information on how Contigs are assembled, see MIT's Guide to Contigs
  

How to use the MIT Chromosome Browser

Select the chromosome of interest using the pull-down menu, then choose the type of data you'd like to see using the radio buttons. Hit the search button.

Once the graphic comes up, you can get more information on any marker, contig, or whatever, simply by clicking on it.

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