NIFTY - Nice Interface For Testing Your Data
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How to use the CHLC search
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:

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.

How to use the Baylor College of Medicine search
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:

How to use the Genbank search
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.

How to use the MIT marker search
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:

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.

How to use the Oligo Vital Stats
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.

Searching for YAC Information

How to use the MIT Yac search
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:

Chromosome Browsing

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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