Hot to get the molecular weight data for a list of proteins once at a time?

Question

[heshamgibriel]

How can I get the full molecular weight and Isoelectricpoint for a full list of proteins once at a time?

I tried to use http://emboss.bioinformatics.nl/cgi-bin/emboss/pepstats,, but I couldn't get the data In columns, as I need to export them In excel sheet.

Is there a command In linux to type so that I could get the data In a much more organized way?

Thanks,

Answer 1

[Ram]

You are using stand-alone pepstats and not the web version, correct? Just run the standalone program using a loop in Linux and store the output in a new output file for every input. That should do the trick.

[heshamgibriel]

I managed to use It and I got the data for the full proteome finally. However, I can't copy/paste the output data in excel sheet as the are not sorted out In columns!!

Should I use python, or there might be some commands that I can type in the terminal to get them all sorted out?

[Ram]

You can use a good combination of grep, tr, cut, sed and awk to get to your desired results, but yes, the task might be better defined and more documentation friendly if you use a scripting language.