Searching for genes by gene properties

The functions in this section are often used to find the ITEP gene IDs for genes for which you know the function or an alias (such as a locus tag) or the location on the genome.

Searching for genes by annotation or alias

You can search for the IDs of genes with a specific annotation using the db_getGenesWithAnnotation.py function. The matches are not case-sensitive:

$ db_getGenesWithAnnotation.py "Phosphofructokinase"
fig|290402.1.peg.581    6-phosphofructokinase_YP_001307727.1_Cbei_0584
fig|290402.1.peg.992    6-phosphofructokinase_YP_001308138.1_Cbei_0998
fig|290402.1.peg.1824   1-phosphofructokinase_YP_001308970.1_Cbei_1843
fig|290402.1.peg.4768   6-phosphofructokinase_YP_001311914.1_Cbei_4852
fig|386415.1.peg.406    6-phosphofructokinase_YP_877380.1_NT01CX_1297
fig|386415.1.peg.830    1-phosphofructokinase_YP_877804.1_NT01CX_1725
fig|931626.1.peg.323    1-phosphofructokinase_YP_005268026.1_Awo_c03330_fruK
fig|931626.1.peg.1249   6-phosphofructokinase_YP_005268952.1_Awo_c12790_pfkA

The first column is the ITEP gene ID for those genes (these are the ones you should use to connect the results to any other functions) and the second is the annotation that matched the query. You can specify multiple annotations to match by just giving multiple arguments to the function, e.g. the following which gives the same results as the above in this case:

$ db_getGenesWithAnnotation.py "1-Phosphofructokinase" "6-phosphofructokinase"

You can also search for genes by alias (e.g. locus tag) as long as those aliases were identified in the original Genbank files. These aliases are appended to the end of the annotations.

$ db_getGenesWithAnnotation.py Cbei_1843
fig|290402.1.peg.1824   1-phosphofructokinase_YP_001308970.1_Cbei_1843