Funny CDS from srs...

Peter Rice pmr at sanger.ac.uk
Mon Nov 27 04:45:51 EST 1995


In article <49893v$hs9 at rc1.vub.ac.be> rherzog at ben.vub.ac.be (Robert Herzog) writes:
>   I have been extracting several hundreds of CDS from various sequences lately, i
>   and found a funny extraction from the MIDMM1 file (from Drosophila) :
>
>   the second CDS srs extracts is as follows:
>
>   MIDMM1  Length: 1536  Check: 5450  ..
>
>	  1  @M at CGACAAT GATTATTTTC TACAAATCAT AAAGATATTG GAACTTTATA TTTTATTTTT
>	 61  GGAGCTTGAG CTGGAATAGT TGGAACATCT TTAAGAATTT TAATTCGAGC TGAATTAGGA
>	121  CATCCTGGAG CATTAATTGG AGATGATCAA ATTTATAATG TAATTGTAAC TGCACATGCT
>	181  TTTATTATAA TTTTTTTTAT GGTTATACCT ATTATAATTG GTGGATTTGG AAATTGATTA
>
>   two or three unusual bases at the start of this one...!

Probably connected with trying to get a translation of it, bacause the
feature table entry is:

FT   CDS             1071..2606
FT                   /note="NCBI gi: 903727" /codon_start=1
FT                   /transl_except=(pos:1071..1073,aa:Met)
FT                   /transl_table=5 /product="cytochrome c oxidase I"

Translation exception handling is in function SlbDoTranslExcept in seqlib.c,
and puts "@X@" into the codon where "X" is the correct amino acid
code.

Of course, this should not happen for display of the sequence, only for
translation. Seems to me that getz does not do translations anyway.
certainly this code should be executed only if needed.

I am not at all surprised LookUp is different - it seems to be a
rather dated SRS version. I am still looking for signs of what GCG
added (rather than the many things left out) in LookUp.
--
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Peter Rice                           | Informatics Division
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