Using Smith-Waterman for comparison of protein sets - (Jul/23/2008 )

Hello everybody,

Hope one of you can help me. I want to compare the proteins encoded by two genomes using SSEARCH. I have downloaded FASTA3 and now I am trying to get this to run but so far I have been unsuccessful. The problem is that I cannot get a results file with all the data of the protein comparison in a single file. When I compare the two protein datasets (both are fasta-files containing multiple sequences) and specify an output-file the program continously overwrites the data in the output-file so that only the last search performed can be found in this file. What am I doing wrong? Does anybody know what I should do?

Thanks very much for your help!

Are you running these programs from the command line? What does the command you're using look like? Usually in circumstances like this, you can specify appending to an existing file rather than creating a new one by using ">>" as the output director rather than ">". So, for example:

my_program input_file1 input_file2 > output_file

will re-create the output file for each iteration. However:

my_program input_file1 input_file2 >> output_file

will initially create output_file, then append future results to it, rather than overwriting it for each iteration.

Thanks HomeBrew! That did the trick... It was driving me mental!