[BiO BB] Affymetrix probe annotation- anyone need to identifyunknowns?
Mike Marchywka
marchywka at hotmail.com
Wed Jun 27 10:05:32 EDT 2007
As an example related to my earlier post, AFFX has this as a class R with
little info
https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=CANINE%3A1606074_AT
(free,but need to register)
with the reference to this:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucest&id=20431335
The automated scripts found these related things- I also have ORF
comparisons
but am just looking at gene/transcript alignments for now.
$ cat likely_hits
/cygdrive/e/new/temp/canis/dcm/1606074/temp
AY656737.1- Canis familiaris isolate 1 breed Basenji mitochondrion,
complete
AY656738.1- Canis familiaris isolate 1 breed Jack Russell Terrier
AY656739.1- Canis familiaris isolate 1 breed Poodle mitochondrion,
complete
AY656740.1- Canis familiaris isolate 1 breed Kerry Blue Terrier
mitochondrion,
AY656741.1- Canis familiaris isolate 1 breed Irish Setter mitochondrion,
AY656742.1- Canis familiaris isolate 1 breed Old English Sheepdog
AY656743.1- Canis familiaris isolate 1 breed Saint Bernard mitochondrion,
AY656744.1- Canis familiaris isolate 1 breed English Springer Spaniel
AY656745.1- Canis familiaris isolate 2 breed English Springer Spaniel
Complete sequence is usually a spurious hit but in this case the entry
could mean something:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=12700659
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=50301805
And the alignment is quite good ( I haven't checked orf's yet but I now
generate
these along with clustalw output for putative matches).
( obviously a proportional space font, like most graphics, makes a mess of
the information...)
CLUSTAL W (1.83) multiple sequence alignment
CANINE_1606074_AT
--------------------------------------------------------ACGC
AY012152
AGGTTTGGTCCTAGCCTTCCTATTAGTTTTTAGTAGACTTACACATGCAAGCCTCCACGC
****
CANINE_1606074_AT
CCCAGTGAGAATGCCCTTAAAATCACCAGTGATCTAAAGGAGCAGGTATCAAGCACACTC
AY012152
CCCAGTGAGAATGCCCTTAAAATCACCAGTGATCTAAAGGAGCAGGTATCAAGCACACTC
************************************************************
CANINE_1606074_AT
TTAAGTAGCTCATAACACCTTGCTAAGCCACACCCCCACGGGATACAGCAGTGATAAAAA
AY012152
TTAAGTAGCTCATAACACCTTGCTAAGCCACACCCCCACGGGATACAGCAGTGATAAAAA
************************************************************
CANINE_1606074_AT
TTAAGCCATAAACGAAAGTTTGACTAAGCCATACTAAATAGGGTTGGTAAATTTCGTGCC
AY012152
TTAAGCCATAAACGAAAGTTTGACTAAGCCATACTAAATAGGGTTGGTAAATTTCGTGCC
************************************************************
CANINE_1606074_AT
AGCCACCGCGGTCATACGATTAACCCAAACTAATAGGCCTACGGCGTAAAGCGTGTTCAA
AY012152
AGCCACCGCGGTCATACGATTAACCCAAACTAATAGGCCTACGGCGTAAAGCGTGTTCAA
************************************************************
CANINE_1606074_AT
GATACTTTTACACTAAAGTTAAAACTTAACTAAGCCGTAAAAAGCTACAGTTATCATAAA
AY012152
GATACTTTAACACTAAAGTTAAAACTTAACTAAGCCGTAAAAAGCTACAGTTATCATAAA
********
***************************************************
CANINE_1606074_AT
ATAAACCACGAAAGTGACTTTATAATAATCTGACTACACGATAGCTAAGACCCAAACTGG
AY012152
ATAAACCACGAAAGTGACTTTATAATAATCTGACTACACGATAGCTAAGACCCAAACTGG
************************************************************
CANINE_1606074_AT
GATTAGATACCCCACTATGCTTAGCCCTAAACATAGATAATTTTACAACAAAATAATTCG
AY012152
GATTAGATACCCCACTATGCTTAGCCCTAAACATAGATAATTTTACAACAAAATAATTCG
************************************************************
CANINE_1606074_AT
CCAGAGGACTACTAGCAATAGCTTAAAACTCAAAGGGACTTGGCGGTGCTTTATATCCCT
AY012152
CCAGGGGACTACTAGCAATAGCTTAAAACTCAAAGG-ACTTGGCGGTGCTTTATATCCCT
**** *******************************
***********************
CANINE_1606074_AT
CTAG--------------------------------------------------------
AY012152
CTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTCACCACCTTTCGCTAATT
****
[ trailer tuncated]
So, if anyone is interested in looking for better id's or could suggest a
better source for annotations or suggest a reason why these hits are
irrelevant, please contact me. It does appear that additional information is
available beyond that posted
on Affx site, at least for the canine array.
Thanks.
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