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getting gene symbol from probe sequence

hello I have a platform(GPL8708 for GSE74930) with this data:

ID     SEQUENCE        RANGE_START         RANGE_END            RANGE_GB 
ECOLIK12_F_00000001    GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTG 2   62   U00096.2 
ECOLIK12_R_00000002 GAAGCTGCTATCAGACACTCTTTTTTTAATCCACACAGAGACATATTGCCCGTTGCAGTCAG   12   73   U00096.2 
ECOLIK12_F_00000003    CGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGG 22   81   U00096.2

... and so on!

I want to get gene names with those sequences. which packages help me(annotate, AnnotationDbi or annotationTools or ...)? Note that this platform isn't AFFY! Thank you!

probe sequence gene symbol
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updated by Sukhi Singh Sukhi Singh • written by vahideh • vahideh

1 answer

Those probes are from E. coli K12 MG1655 genome and also here. Feature table for that genome is here. You have the start and end coordinates in your file. An intersectBed type strategy should give you the names you need. This appears to be a tiling array so all entries in your file would likely not get a gene name.

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written by GenoMax GenoMax

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