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7 days ago

Hello! I am totally new to STRING and am trying to open files downloaded from STRING protein networks. Is there any way to open these without using Linux and R. i.e. I have started to use 7zip and it doesn't help it looks like it has extracted the file but it is hard to understand?

this is a sample from the protein.links.detailed file am I doing something wrong. should I have used winzip!? it seems all files seem to have been converted to 7zip type by me just opening 7zip and using it once! I don't have the training in R so not sure how I will read the file. I appreciate any advice! See the sample of file contents below:

protein1 protein2 neighborhood fusion cooccurence coexpression experimental database textmining combined_score
9606.ENSP00000000233 9606.ENSP00000272298 0 0 332 62 181 0 125 490
9606.ENSP00000000233 9606.ENSP00000253401 0 0 0 0 186 0 56 198
9606.ENSP00000000233 9606.ENSP00000401445 0 0 0 0 159 0 0 159
9606.ENSP00000000233 9606.ENSP00000418915 0 0 0 61 158 0 542 606
9606.ENSP00000000233 9606.ENSP00000327801 0 0 0 88 78 0 89 167

opening protein files STRING network • 244 views
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7 days ago
GenoMax 104k

This seems to be a tab or space separated file. You should be able to open it with a text editor or Excel after you uncompress it with 7-zip.

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Genomax, thank you for your advice, I will try this again! I opened it in notepad ie as above this is how it looked. I will try to open in excel- thanks again, MUCH appreciated! I will let you know how I get on! Fiona

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Dear GenoMax, I am still having some trouble I tried excel-> data--> txt file and it opened with one word on one column not sure what I have done wrong can you please help? i chose "fixed width", "column data general" and it says "text file has more data than will fit" this is what the top of the excel document looks like: with a few words in each column ie rh in one column. any advice will be greatly appreciated!

group1  group2 n    eigh    bo  rh  ood fusion cooccurence coexpression experimental database textmining combined_score
COG0001 COG0002 250 0   0   48 0 0 151 341
COG0001 COG0004 123 0   0   0 0 0 101 178
COG0001 COG0005 130 0   0   0 0 0 0 130
COG0001 COG0006 155 0   0   75 0 0 229 346
COG0001 COG0007 596 0   1   42 100 376 0 499 884
COG0001 COG0008 126 0   0   124 0 0 499 584

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You should choose "delimited" as you import the file into excel. You may need to try "tab" or "space" as delimiters in relevant dialog options. You should be able to see the preview of what the data would look like and thus be able to choose correct delimiter.

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thanks GenoMax I will try this sorry for delay in reply!! Fiona