New features in FAST-MAP v1.04b

There are numerous new features and functionalities provided by FAST-MAP v1.04b. Here is a list of the major changes:

Analyzing studies

A study is a collection of gels. In FAST-MAP, a "study" is treated exactly the same as a "gel":

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View families

The user can now provide family information in a LINKAGE-format file called pedigrees in the "user/" directory. A FAST-MAP utility, add_pedigrees , can be used to automatically extract pedigrees from sample names with specific formats. Then, in allele_view , the user can click on a View Family button to display the genotyping results of all the individuals in the same family in a single window. This is a useful tool for detecting mis-allele calls.

However, note that FAST-MAP does not make use of any pedigree information in genotyping -- the alleles are called solely based on the electrophoretic data. In a future version of FAST-MAP, we will provide Mendelian inheritance checking functionality and flagging the suspect genotypes that failed the inheritance constriants.

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Running FAST-MAP on a Macintosh

We have successfully ported FAST-MAP to run on Macintoshes. The same code that runs on Unix also runs on a Macintosh. Please see "Installing FAST-MAP on a Macintosh" in the user manual for specific instructions. We are planning to port FAST-MAP to the PC platform in the near future.

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Creating "layout" from ABI sample files

FAST-MAP is now able to extract sample names from ABI sample files to create the "layout" files for the gels.

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New programs

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Old programs with new names

These are the programs that have their names changed:

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Obsolete programs

In the previous versions, to batch process more than one gel, the user has to use another program with a suffix "_set". For example, to call the alleles on more than one gel, the user has to type "allele_call_set GEL1 GEL2 ...". In FAST-MAP v1.04b, multiple gels or studies (up to 45 of them) can be entered to the same program. For example, "allele_call GEL1 GEL2 ...". However, all the viewing programs only take in one gel or study at a time.

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Improved interface

We have improved both image_view and allele_view. For image_view in which we have completely re-designed the interface and added new functionalities. Please read the sections on "Image_view" and "Allele_view" in the user manual for details.

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Changed user file formats

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Pharmacia data

FAST-MAP can now analyze the ALF data files from Pharmacia. Currently, only HP9000/700, Sun4, and Solaris 2 are supported. Because of the single-dye system, additional information and specific layout may be necessary to produce accurate sizing and genotyping results. We are currently experimenting with ways to improve the genotyping accuracy on such data. Please contact us if you are keen on using FAST-MAP to analyze data generated by Pharmacia machines.

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