Finding common genes

Question

[div]

Hi all,

I have two list of genes in txt format from S. aureus genome which are generated from RAST Server and PGAAP Pipeline.

Now I need to sort this list by which I can get more number of common genes from both the files.

Is there any way to check for each gene in one file whether it is present in the other file?

Linux or windows suggestions are welcome.

Thank you in advance

[iraun]

Do you need to get the common lines (genes) between two files? If the answer is yes, read about sort and comm linux commands.

[h.mon]

How is the format of your lists? There are many ways of doing this, but it help to know how your data is formated.

[div]

The gene list is alphanumeric which also contains special characters. In the given list I should remove all the numbers and also special characters and after removing all these it should only contain alphabates except for the EC, FIG.

Example of the gene list:

Formiminoglutamase (EC 3.5.3.8)
FIG01108370: hypothetical protein
Ribose 5-phosphate isomerase A (EC 5.3.1.6)
Uncharacterized protein conserved in bacteria
Aldose 1-epimerase (EC 5.1.3.3)
Protein of unknown function UPF0060
ABC-type Na+ efflux pump, permease component
ABC-type transport system, ATPase component
FIG01108220: hypothetical protein
DNA-3-methyladenine glycosylase II (EC 3.2.2.21)
Sodium/glutamate symporter
Isopentenyl-diphosphate delta-isomerase, FMN-dependent (EC 5.3.3.2)
Magnesium and cobalt transport protein CorA
3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)
FIG01107838: hypothetical protein
putative esterase
FIG01108339: hypothetical protein
Membrane component of multidrug resistance system
Multidrug resistance protein [function not yet clear]
TetR family regulatory protein of MDR cluster
Teicoplanin resistance associated membrane protein TcaB
Teicoplanin resistance associated membrane protein TcaA
Teicoplanin-resistance associated HTH-type transcriptional regulator TcaR

[h.mon]

Did you try rbagnall solution? Should work, or get you pretty close to what you want.

Answer 1

[rbagnall]

grep -wFf file1 file2

Grep A Pattern From File

[h.mon]

I think for a list of gene names like his, grep -xFf file1 file2 is better.