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Human Genome News Archive Edition

Human Genome News, March 1992; 3(6)

GDB and OMIM Solutions

This column will appear periodically in Human Genome News to feature answers to questions that Genome Data Base (GDB) and Online Mendelian Inheritance in Man (OMIM) users frequently ask GDB User Support. For help with other questions and problems or to offer suggestions, readers should contact their local User Support office.

  • How do I find microsatellite polymorphisms?

Answer: Direct retrieval of polymorphism data is not possible, but this data can be found by retrieving loci that are polymorphic. On the RETRIEVE LOCI screen, enter "sat" (for satellite) in the Variation Type field. Data in other relevant fields can also be entered. For example, to retrieve microsatellite loci on chromosome 5, enter "5" in the Location field. To see related allele data for a specific locus after the polymorphic loci have been retrieved, use the Call menu option to enter the Polymorphism Manager and then the Alleles and Allele Population/Frequency Managers.

  • How do I find all the CA repeat polymorphisms on chromosome 21?

Answer: As stated in the previous example, polymorphism data cannot be retrieved directly; loci that are polymorphic must be retrieved first. The appropriate code for (CA)n is "dinuc" (for dinucleotide repeat). To see all the code choices for the Variation Type field, move the cursor to that field and select Field Values. On the RETRIEVE LOCI screen, enter "dinuc" in the Variation Type field and "21" in the Location field. Boolean operators can be used in the Variation Type field; enter "tri or tet" for polymorphisms with tri- or tetranucleotide repeats.

Once the polymorphic loci with dinucleotide repeats have been retrieved, call the Polymorphism Manager for each locus. Since a locus may have several types of associated polymorphisms, check the table view in Polymorphism Manager for those with dinucleotide listed in the Polym Type column. The Annotation field (detail view) includes information about the specific repeat pattern [e.g., (CA)n].

  • How can I get past the 9th allele of 15 alleles for the Mfd139CA/Mfd139GT probe?

Answer: Viewing allele band-size data involves moving around a matrix. Use the Go To menu option to display other alleles and band sizes not shown on the screen. (The > and < symbols indicate that more band sizes occur.)

The Go To submenu includes Next, Previous, First, Last, Left, and Right. Select the direction in the matrix you want to go. Left and Right will move horizontally to display different band sizes. Next, Previous, First, and Last will move vertically to display different alleles.


HGMIS Staff

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Human Genome Program, U.S. Department of Energy, Human Genome News (v3n6).

Human Genome Project 1990–2003

The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.