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22 chromosome comments


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Comments and examples

Comments to the human chromosome 22 article (Nature 402, 489; 1999).

When we carefully evaluated the results from the article (as presented on the website of the Sanger Centre) and when we compared our results from the RepeatMasker program and the Repbase database, we observed that many individual items attributed in the chromosome 22 article to different HERVs are in fact parts of one integrated retrovirus. Fusion of the fragments decreases the total number of HERVs.

On the other hand the HERV group in Table 2 does not contain all internal retroviral sequences (for instance HSRIRT, also known as HERV15 in the Repbase, or nine MERVLs that are in fact related to HERVL). The LTR group in Table 2 contains LTRs of retroviruses as well as other LTR-transposons (especially MER4 group), and so part of the LTR group should be listed for example as HERV-LTR. Some of the HERV-LTRs are for historical reasons named MER (e.g., MER9 and MER11) and MLT (MLT2 group) and are listed in Table 2 in the corresponding repeat types.

When these corrections are made, the total number of internal HERV sequences (group HERV in Table 2) decreases from 255 to 153, but the total coverage increases from 0.48% to 0.58% and the overall retroviral sequences reach 1.45% (489,426 bp). The following entries can thus be changed in Table 2:

Repeat type Total number Coverage (bp) Coverage (%)
HERV internal sequences 153 196,797 0.58
HERV LTR 716 292,629 0.87
HERV total 803 489,426 1.45

Examples of fusion of data from RepeatMasker

  • Example 1
  • Example 2
  • Example 3
  • How to interprete RepeatMasker outputs
  • Our data were obtained using the latest available version of RepeatMasker (v04/21/99) and with the Repbase (v3.09) with some additional filtering described here.When we used unfiltered RepeatMasker output (.out file), the overall coverage of retroviral sequences reach 1.81 %. There are 1112 of "raw" elements. This number becomas smaller when corrections suggested in our examples are made.

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