[Genome] mRNA Track

[Pauline Fujita]

Dear Prof. Kim,

The BLAT results are displayed according to the identity as you
described, but they are also subject to a length criteria. For the Human
assembly, a search result must be at least 25% of the query in length to
be retained and in this case the the 283bp piece found by BLAT on
chromosome 20 is only 21.4 % (283/1321 bp) of the query in length:

BLAT Search Results
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN
---------------------------------------------------------------------------------------------------
browser details YourSeq 1022 279 1303 1321 100.0% 17 + 56800468 56824974
24507
browser details YourSeq 281 1 283 1321 99.7% 20 + 48844838 48845120 283

For assemblies of lower quality this length requirement may be different
(i.e. it is not 25% for all assemblies). Hopefully this information was
helpful and answers your question. If you have further questions or
require clarification feel free to contact the mailing list at
genome at soe.ucsc.edu.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Prof. Sangsoo Kim wrote:
> Dear sir,
>
> The GenBank mRNA track shows AF361221.1 on the human chromosome 17,
> missing the 5' 278 bp.
> It does not show the missing part in any other part of the human genome.
>
> If I 'blat' the mRNA sequence against human genome, I can see that the
> missing part can be aligned with 99.7% identity.
> According to the Methods describing how the alignment was made, the
> alignments having identify within 0.5% of the best match and higer than
> 96% are to be kept.
>
> I wonder why the 5' part the sequence was not captured in the track.
>
> Sincerely,
>
> Sangsoo
>   
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