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CEPH Mega YAC clone


Information


Search for CEPH Mega YAC clone

Following process is maybe not best but how we find the particular YAC clone containing locus of interest by STS marker information.
Because end sequences of the YAC clone have not analyzed, the YAC clones are not mapped on a genome browser.
We show a case for human IGL locus (Gene ID: 3535, 22q11.2) as an example.

  1. download “07-97.YAC2STS.txt” data file at
    ftp://ftp.broad.mit.edu/pub/human_STS_releases/july97/
    to your computer. This file contains YAC clone ID with corresponding STS hits.


  2. STS are positioned to the human genome available at the “UCSC Genome Browser”.
    Visit UCSC genome browser web site.
  3. Chose “Human GRCh38/hg3”.

  4. Set region of chromosome and then click “go”.
  5. Set options as indicated below and click “refresh”.
  6. STS markers will show up on top panel.

  7. Click STS name. Click the right button of your mouse to “Open details page in new window…”.
  8. STS maker info will show up.
  9. Please find “STS Marker, Start, End and Other names”.
  10. Copy these items to a table of Excel file.

  11. Find the STS marker and corresponding YAC in the “07-97.YAC2STS.txt”.
    I hope you or your colleague can handle MS-DOS command. The following text is an example of a batch file.

        set target=”07-97.YAC2STS.txt”
        echo “RH48655” >result.txt
        find /I “RH48655” %target% >>result.txt
        echo “STSG30889” >>result.txt
        find /I “STSG30889” %target% >>result.txt
        echo “WI-362” >>result.txt
        find /I “WI-362” %target% >>result.txt
        echo “D22S636” >>result.txt
        find /I “D22S636” %target% >>result.txt
        echo “AC22-362” >>result.txt
        find /I “AC22-362” %target% >>result.txt
        echo “PH838” >>result.txt
        find /I “PH838” %target% >>result.txt
        :
  12. Put YAC ID to the Excel.
  13. The clone you find now maybe include false-positive. So please find the clone which hit multiple STS of locus. With this way, you may find the clone usable for your research at last.

(RDB04215 2004.02.13 T.M.)

2019.08.12